I see what you mean but my understanding was that in my case it wasn't to pick up "cannisters" of transmissions but rather "intercept" them - ie. when I dropped out of supercruise something "pinged" and I got the comms top left telling me that I'd done what I needed to (there weren't any cannisters floating around as far as I could see!)
This was supported by the fact that the mission on the bulletin board seemed to suggest that I'd done what was necessary - it was just the "Give Cargo" button that was "redded-out"!?!?!
Yer, you will often get a counter offer from another ship and it is up to you if you choose the counter offer or continue on with your original mission.
When it says"Intercept Rebel Transmissions", it means pick them up and take them back to that station/dock. The rebels drop the cannisters for someone to pick up and then clear off. There will be no ships about when you fly to the correct USS and will just be white blocks on the radar and when you lock on with your cargo scoop open, you will see if it is Toxic waste/Art/Rebel transmissions/Military plans etc and if it isn't what you need, ignore or pick up and sell on the black market (make sure you have enough space for the actual amount of pickups you need).