things that bother me are typically small script issues, not plot stuff. there could be a 500 page thread about movie plotholes. stfu and enjoy your popcorn, it's a movie.
here are a couple that bother me when i hear/see them.
in jerry maguire, during the cardinals v cowboys game when cuba gooding gets hurt, one of the announcers (gifford?) says something like "well, at a time like this, you just hope his family is not watching this."
ok, i know he's not an actor, but come on. it's the end of the season, cardinals are hot, challenging the cowboys for the division, he's the star player having a breakout season, and they're playing a close game on monday night football. yeah, his family probably has a lot going on, they'll just read about it in the paper the next day.
another one is old school. they have a big party, and it's clearly friday night. will ferrell talks about how he can't drink because he has "a nice little saturday" planned in the famous bb&b/home depot scene. then the next day, everybody is back at the office, kids (both high school and college) are back in class. it's a fucking saturday and it's not that hard to write it that way.
also, for the "a few good men" mentions, he didn't need the big payoff to win the case. he had the two conflicting orders - that's where jessup got caught. "sometimes men take matters into their own hands", "no, you made it clear your men never take matters into their own hands, your men follow orders or people die."