This is not quite the same as "movies that just make no sense whatsoever," mind you.

What happens is, some movies have rather muddly plots that clear up with repeated viewings and analysis.

Other movies have plots that initially make sense to you, where you just accept one thing after another, caught up in the narrative flow, but what was crystal clear becomes incoherent when subjected to close scrutiny, when you already know the plot and have time to look deeper into the internal logic.

For me, giant spider invasion was like this. At first, it seems a straightforward B monster movie. There's some rocks falling out of the sky, spiders hatch out of them, scientists babble about a doorway in space, giant spiders ensue, kill the queen, badda-bing. It's only later that I realized there's no real follow up to the "black whole" thing, nor would killing the queen solve all their problems (they still have lots of other spiders which will presumably grow to enormous size).

The movie Lifeforce also ranks really strongly here, and Rise of the Silver Surfer has a major rewatch-apparent plothole.