Here are my nits, not in any particular order:
(1) Col. Dubaku - (a) How did he survive that grenade blast just a few feet from him? And not just survive, but look completely uninjured merely a few months later? No burn or shrapnel scars at least? (b) How the heck did this war criminal get into the country at a time like this?! Isn't it enough to show in each season how many traitors we have in America at all levels of the government and the general lameness of our security and law enforcement officers? (Okay, I realize this is a silly question; I'm sure he got smuggled in by those super well connected folks in the government. How does one find so many powerful traitors every few years?)
(2) So Chloe and Bill stole all that fancy high tech security equipment from the former CTU? Because if not, where the heck did two unemployed civil servants get/afford all that! (I say unemployed since they are apparently doing this full time. Which raises another question -- how can they afford to do this?)
(3) Jack flying off the handle within minutes of provocation by Tony. This is not a really a question, just a suggestion. Please, writers, does he have to always rush across the room and do that choke hold? Let him have some other means of expressing his anger management issues. I know that is considered his trademark move by now, but surprise me on occasion. He doesn't have to be THAT predicable, does he? At least wait until the third or fourth interrogation.
(4) Jack and Tony gets out of the FBI "perimeter". How lame was that perimeter? It ended at the darn attached garage?!!! (Remember that agent reported in saying they "got through the perimeter") Come on. Didn't Agent walker order a 5 block perimeter? When I asked this question DH said "the FBI must have hired all those former CTU agents who always let bad guys/gals through their perimeters." I think he is right.
ETA:
(5) I am bothered by how our entire country -- all of our infrastructure -- can be put at risk with a small portable computer part that is so easily assembled.