Weirdest theater experiences I've had were Fathom Events screenings for Yu-Gi-Oh The Movie and a dub double feature of the Sailor Moon R and S movies. Mainly because they were mostly empty.

Though I do remember Sailor Moon R starting a bit late, prologue was cut off.

I do recall one experience where I was watching a movie (I don't remember which) and there was a scene where sirens were going in the movie. It just so happened that at the same time, the fire alarms of the actual theater started during it. A staff member rushed in yelling to get out of the theater, and those of us in the theater thought it was a prank, however it turned out not to be a prank. Instead it turned out later to be a minor issue since the theater cooked and sold fresh pizzas to eat, and one of the cooks had accidentally left one of the oven doors open for a little too long, causing some smoke to reach the fire alarm, setting it off. There was no actual fire, luckily. But still, we had to go outside the theater and fire trucks arrived for nothing. Didn't even get a refund for the rest of the movie we missed because of that. The whole experience was weird at the time.

I think another weird movie theater experience of mine was going to see Watchmen and there was a bunch of kids there. I was like, this is a R-rated movie, folks. The audience reaction was funny too. There was always like a WTF reaction from audiences when certain scenes happened.