You can say any of the three! "At what time is the movie?" sounds a bit more formal, but all three mean the same thing and are correct.

They're all grammatically correct; they're all just variations. Just take note of using the prepositions. It always depends on the speaker how they want to express themselves. Take note on the second sentence that you are asking the time of the movie at a certain/specific place; you need to add a location. What time is the movie at WHERE? What time is the movie? The movie starts at 5pm/ The movie is at 5pm. What time is the movie at the cinema? It's at 5pm. What time is the movie at Bob's? It's at 5pm. (Bob's house) At what time is the movie? Hmmm.... It's at 5pm.