I saw this posted on a different forum, and it does seem to have a few good answers for some of the questions that cropped up during the film:
SPOILERS BELOW!!!!!
1.) What was the mothership? An alien convict ship? An alien slave ship?
The ship was a long distance resource and mineral collecting structure. Blomkamp explains: “Obviously, there's much more of a population on the main planet, but the ships will go out and get the minerals and the ore and whatever resources they need and then bring them all back home.” It is actually part of an even bigger structure. “The other thing is that the ship was meant to clip together with other ships. So there's, like, vast amounts of resources that they're bringing to the parent planet.”
2) Why did the mothership cruise to a stop above Joburg? Did it run out of fuel?
No, the mothership did not run out of fuel. After the queen died, the mothership cruised to nearest life-sustaining planet. Blomkamp explains: “…it was the ship that realized that, unless it gets to a life sustaining planet everything is going to die, which is a cool idea. So the ship just auto pilots to the closest one in the Goldilocks band, and it's our planet and then pulls up and hits the breaks.”
3) What falls off the mothership when it first makes contact with Earth?
The command module to the mothership. In the movie, it is shown to fit into the mothership like a perfect puzzle piece.
4) Why does the command module fall off?
Not explained. There are many speculations, however. Maybe whatever virus, disease, or entity that killed off many of the prawns lead to a malfunction or lack of maintenance in the mothership. Or maybe, when the queen dies, the mothership is programmed stop near a life-sustaining planet and detach the command module so that the worker drones do not attempt to pilot it and get themselves killed or waste valuable resources. Or maybe the mothership was programmed to respond to threats like holes being ripped open in the mothership and detach the command module to save the more valuable, intelligent prawns inside.
5) Why didn’t scientist rip apart the mothership and examine it like they did to countless prawns in the medical labs?
Because unlike the dead prawn subjects, the mothership is a threat hovering
above Joburg. The scientists could not comprehend alien technology. One false move could lead to the entire mothership crashing down upon the populated city.
6) Why doesn’t the military shoot down the mothership? It is a threat.
It is more of a threat when it is a flaming fireball falling upon Joburg. See FAQ #5.
7) Why would the prawns not come out of the mothership for three months if they were malnourished? Did they want to die or something?
The prawns do not operate like humans. They operate more like a hive society. Although with proper leadership they were able to achieve amazing technological feats, without their queen they were simply individual worker drones that were unable to get much organized. Much less make first contact with a new species.
8) How come only the queen (or smarter leaders) died but the less intelligent prawns survived?
The worker drones were more immune to disease because they were bred to be physically tougher, not mentally capable. Blomkamp explains: “And the ship, when the army generals or the queen of that particular ship died off by some sort of virus or bacteria that they picked up on some other planet, that killed them off. And it didn't effect these sort of resilient, hardy sort of drone workers.”
9) Who built the slums in District 9 right over where the command module fell? Very convenient.
The slums were already there. Many people were relocated from the slums when the prawns first made contact, because rights and property for the prawns was a big issue back then. The only change is that District 9 was segregated and walled off from the rest of society. Explained in the introductory documentary style clips.
10) Why did the prawns not resist? Not all of their weapons were confiscated. They would have easily defeated MNU security forces with their superior weaponry.
Yes, they would have. But without their queen, they were unable to band together any form of effective resistance. Blomkamp explains: “Also, it [the hive mentality] sort of explains why they don't turn on the humans. Individually, they may be feeling oppressed, but they don't have it together enough to form a resistance and back one another. So I found that really interesting.”
11) How were the Nigerian forces able to hold gang operations in District 9 when it is secured by MNU?
District 9 was very loosely secured by MNU. This was exemplified in the movie
by prawns able to sneak out of District 9 although they were prohibited and Wikus easily sneaking into District 9 when he was a fugitive on the run.
12) Why couldn’t any prawns help Christopher gather fuel but his friend and his son? Don’t they want to leave?
The majority of the prawns were worker drones. Without their queen simply seeking survival, unable to formulate any sort of plan. See FAQ #7.
13) Well then why was Christopher so special? I thought the queen (or the leaders) all died. And if he was so sharp, why did it take him 20 years to get his stuff together?
A hive is programmed to adapt a new queen or some sort of leader, but after some time after the queen's death, not right away. Blomkamp explains: “There is a subconscious hive mind happening, really what they should do is lay one egg that has a different embryo in it that grows into a Queen or being someone that dictates direction. But I think in the interim, because they may have done that, there may be an egg out there with that, but as that being is growing, I just like the idea that he may have been a lot more directionless in the beginning. But the hive structure of their society may just pick one or two that starts to become the leader. Like the overall structure of his brain may change because the hive may want that to happen. So he starts having a direction and a goal. Which is an interesting idea and it's just enough to kick start them to be able to get to the ship to get back.”
14) Even so, when Christopher does realize to take action, why are he and his son alone in searching through the heaps of garbage for prawn technology? Why not persuade the rest of the prawn species to help find technology as fast as they can?
Christopher kept his operation extremely secret to ensure that he wouldn't get caught. If caught, he knew MNU agents would confiscate any prawn technology he had no license for, and all of his work would be lost. If he hired hundreds of prawn to help him in his search, at least one would be bound to reveal something to MNU. Hundreds of prawn suspiciously rallying back and forth between a single shack would be a spectacle quite hard to miss. He let one of his trusted friends help him in his search, and even that was dangerous, as shown by the prawn who gets shot in the beginning of the film.
15) Even so, why search through garbage for prawn technology when he could just borrow it from dozens of his friends that have been selling prawn weaponry to the Nigerians?
Christopher probably did not require the materials that constituted prawn weaponry in order to make the fuel. And even if he did, he already obtained all the prawn weaponry he needed because dozens of weapons were shown to be stashed in his shack. He was probably searching for different prawn technology outside the category of weaponry.
16) Why couldn’t Christopher just jack a chopper and fly the mothership away?
The mothership cannot be flown without the command module.
17) Christopher says he needs the fuel to fly the mothership away yet little CJ pilots the mothership from the command module without fuel. What’s that all about?
The mothership already had fuel. See FAQ #2. The fuel Christopher was gathering for 20 years was for the command module. The command module pilots the mothership like a remote control can pilot a toy car. It can also activate highly armed mech suits.
18) If the mothership needs fuel so badly, how is it hovering above Joburg for two decades? Plot hole!
Once again, the mothership already has fuel. See FAQ #2.
19) So this fuel magically transformed Wikus into a prawn? Very convienient.
The biological goo-like substance containing alien DNA powered most of their technology, such as their weapons and the command module to the mothership. It is based off of prawn DNA, so if exposed to internally, it can actually alter another species’ DNA to integrate that of a prawn.
20) How in the world do Wikus and friends talk to prawns?
The prawns have lived integrated with human society for over 20 years. Because the new species was so heavily impactful, many humans must have learned to understand the prawn language in that time period. Especially hired MNU workers serving as ambassadors between the two species. It is important to note no species learned to speak the other's language, only understand it. Humans did not speak prawn, but they understood it. Prawns did not speak human, but they understood it.
21) Why three years?
No explanation. I guess this is the amount of time Christopher needs to make a round trip to his planet and then back to Earth, with some sort of species saving in the middle.
22) What was the point of attempting to put fuel into the command module and fly up to the mothership if the tractor beam could have just picked it up all along?
The command module controls all of the technology on the mothership. Without fuel in the command module, Christopher would not have been able to activate the tractor beam in the first place. In addition, being lifted via the tractor beam is much slower than actually flying the command module to the mothership. The only reason it worked is because Wikus held back MNU forces with the mech suit.
23) How was the fuel that transformed Wikus' DNA into prawn DNA supposed to fix him? Why won't Christopher just fix him right away? Why wait three years?
Contrary to popular belief, Christopher was not going to use the fuel to fix Wikus. He states that he was going to use the "medical machines" aboard the mothership to fix him. However, the command module controls all of the technology on the mothership, including the medical machines. See FAQ # 22. The reason Christopher did not want to fix Wikus right away is also stated in the movie. He did not want to waste the command module's fuel activating anything besides what was absolutely necessary to get them back to their home planet.
24) What were those scorpion-like creatures duking it out in the little arena? Those definitely weren't from Earth. Are they baby prawns?
They were not baby prawns. Actually, they were the prawn equivalent of pests or rodents found aboard the mothership.
25) Why didn't the rest of the world powers step in to organize and take control of the prawn situation? After all, this is first contact, a worldwide historical event.
As historical as the event is, it does not change the fact that the mothership landed in South African territory, which legally leaves the prawn situation in South Africa's control. To take control of the prawn situation, a nation would have to invade a Democratic state, losing favor on the global scale.
26) I don’t like the main character. He aborted alien babies. He threatened to take Christopher’s kid away. He hit Christopher with a shovel or a gun or something. He killed innocent MNU agents. He’s a jerk!
Okay.
, they seemed like a bunch of ******* (cats), it just wasnt rite 
Later in the film Wikus traps christopher outside and attempts to fly away, while christopher is under threat of being shot, but the marine waits and waits and waits oh then finally the ship takes off and he has to run away, hooray christopher lives again. 
