There’s always a degree of suspension of disbelief when it comes to movies, but usually their editorial liberties don’t ruin the immersion and entertainment. Like anything however, there are limits, particularly when it makes the plot of the movie fall apart.
These movies, while all great on their own merits, have moments that make most of the experience fall flat when you think about it for more than two seconds. Of course, expect heavy spoilers for most films listed, since you can’t know if a plot hole affects a film without having watched it.

The Dark Knight Rises (2012)
At the end of the movie, Batman ‘sacrifices’ himself to stop a nuclear blast from destroying Gotham. He obviously survives, but it isn’t clear how he did so, unless he had a teleporter on his batbelt.

Jurassic Park: The Lost World (1997)
The movie starts with a ship without crew, seemingly slained by something. But the only creature that could’ve done it is the locked away T-Rex, so what took out the crew?