It seems like spiderman and MIB break down a lot. It seems like on MIB, something little will go wrong, and the ride will be down for a few hours (like someones seatbelt comes off). spiderman seems to be the test track of universal. Every time you go it's always messed up in some way where they have to close down the ride. I too have gotten stuck in the water scene. The car sat there and the movie played through about 5 times (cool to see it when our not moving. The perspective constantly changes on the screen because the cars normally move). Then it stopped for about 10 minutes, and then it started up again. Most of the other times the pause in the ride is less than a minute, then you get started again.
I've also gotten stuck on Dueling Dragons, the hulk, dudley do right, jurassic park, cat in the hat, and Posidions fury. Nothing ever at Universal Studio.