Things that bugged me about the movie:
* Where was Number One? Other senior officers were getting sick, or killed, or not-knowing-Romulan, so it shouldn't have been too difficult to get rid of her to make Spock Captain. Or you could've given her her own ship, or put her somewhere at the Academy, or something. Was she hiding somewhere and I need to watch it again to try to spot her?
* Why was Lieutenant George Kirk's pregnant wife on the starship? Families being on ships was a big thing for TNG. If he was Ship's Captain, then yea, there's precedent for allowing a Captain's Wife on board. But he's not. Is she in Starfleet? There's certainly no hint of that. No 'Breathe, lieutenant' or 'Here's your baby, Ensign'. And if she was, then why is James Kirk all 'Oh, my Dad was in Starfleet'. Yea, what about your Mom who raised who? What was she? And why was she on a starship? Was she part of a mission? Rescued from somewhere? Envoy to somewhere? Civilian specialist of some sort?
* Why are they building starships in Iowa? (Or maybe it wasn't in Iowa, but it was somewhere in North America, and my point is.. why on Earth?) Starships aren't designed to sit on the ground. It's not exactly stable in Earth gravity. What is the energy expenditure to build a starship with antigrav equipment everywhere to get the job done? How are you getting it into orbit when you're done? In short, what the frell? That didn't even look right.
This isn't a problem, but a question...
* Spock and Ambassador's Spock's noses looked really, really similar. Which one had the makeup on to achieve that?
But maybe part of the appeal of Star Trek is nitpicking it. As the canon grows and grows, it becomes a more complex task to nitpick. Easier, in one sense, as they're more likely to get things wrong. But harder, because you have to know all this esoteric trivia, like Starfleet policies and matter/antimatter intermix ratios.
Which is why it's fun to snigger at McCoy's bisexual tribbles, to wonder how Picard acquired a British accent, to formulate theories about different races of Klingons, and to be annoyed at people "de-evolving" into lizards.
If we couldn't nitpick, would it not be Star Trek?