I've got my gripes with some of the story choices they made, but nothing to the point that it hurts my enjoyment of the movie--certainly nothing that stands out unless I stop and think about it.
If I was being hyper critical of the movie, I could tear it to shreds. But I can do that with just about any Star Trek movie--or movies in general. And, frankly, that fun from time to time, but it's not fun to be in the mindset 24/7 when it comes to a movie.
I prefer to nitpick-to-death a movie I love. If I don't like a movie, I just don't watch it. Seems the logical thing to do. Now, I do tear down movies when people insist such-and-such movie has no plot holes/is superior to another movie in a series, because that's fun, but it's not malevolent in nature.