they were doing the jumps initially to get away from the Cylons (we later discover that this was because one of the civvie ships was being tracked) - the very minor but slightly annoying point that bugged me was that they let the civvie ships jump, then a few seconds later they jump, then an order is given to start the clock... so we've introduced some random delays in our timing process yet the Cylons appear at exactly 33 mins - yes it is pedantic...
it was a bit odd that they took 200+ jumps to consider things like splitting the fleet, jumping to diff locations then re-grouping
now the slightly less nit picking ones:
this is supposed to be a bit like an aircraft carrier yet the main officers are pretty much all pilots or ex pilots in the case of the commander and XO - there is like one main cast member who is an officer and not a pilot - the technical guy who helps Dr Baltar...
when they need to interrogate a Cylon they don't send over an intelligence officer or NCO... they send a pilot!
when they need to provide security for their new parliament thing - the people in charge of providing it aren't say the marine corporal we've met briefly before, someone with comprehensive small arms training, but two pilots (Apollo and Starbuck)??? Though we do see the marines wandering about aimlessly a bit.
oh and they later have a bit of a party on board that luxury civvie ship - who is in attendance, together on the same unarmed ship: The President, the commander, the XO, Apollo - the head pilot/CAG, Starbuck - their best pilot - this is when they're in a scenario where these cyborgs could pop up at any moment and all the most important people are together on the same unarmed ship, leaving god knows who in charge of Galactica and any decision to launch alert fighters, jump etc. etc.. should Cylons appear.
it does seem the ships are all a bit too close together - then again I guess this is TV
likewise this goes for the dogfighting too - these days fast jets will engage each other over the horizon so I'd have expected spaceships could engage with each other before coming into visual range... granted that would be less exciting so we're going to suspend belief and pretend that weapons technology hasn't progressed since WW2 and they have to blast each other at close range with the equivalent of unguided machine guns that they crudely aim by moving their ship - then again I guess it is TV etc..
they discover a new planet and want to send people down to explore - do they send the marines they have on board... you know the ones with infantry training etc.. nope they send the 'chief' and his engineering crew to accompany Dr Baltar all lead by... yup a pilot! They do throw in a bit of realism whereby the young officer/pilot is a bit clueless after the accident and the senior NCO, the 'chief' needs to strongly advise him
don't get me wrong I love the series and it is the plot/acting that I'm most interested in - but things like this do take a little away from the realism(yes I fully appreciate it is sci-fi)
edit - oh and lastly, that captured Cylon vessel with the dead Cylon fleshy stuff inside - surely if that dead Cylon-thing was pulling the levers etc.. and she's got that figured out then they could clear all that flesh/gunk out of there now?