Liking a movie, or any media, doesn't equal liking every single aspect of it. A lot of us surely do feel that no movie is entirely flawless.
For me, one such moment would be the explanation for how you die for reals if you die in The Matrix. "Your mind makes it real" is just a copout. Your brain simply doesn't have that power, or anyone with violent dreams would be a goner.
What's your "meh" moment in movies you otherwise enjoy?