I've seen Fantasmic! just as you have described last July, it was stopped 3 times. Was rather amusing.
As for the Evil Queen debate, I do believe you. If you watch to the far side, you'll see someone come out of the cauldron (old hag), and hug the wall, and the evil queen disappear down the cauldron.
If the trap door is broke, then this transformation can't take place, therefore the evil queen will normally put some sort of wig/headpiece on. Clearly this is what happened when you saw it, this is also backed up by Mickey not being in the usual centre spot at the end and being off to the side.
My friend saw it on Thursday and said she saw the exact same thing you are describing with the evil queen.
I've seen many, many shows at Disney, but all the problems seem to happen at Fantasmic!
(Boats with monkeys crashing into each other, screen projections not working, no Maleficent so they have Mickey standing there being scared whilst she talks etc). The boats in Pocahontas scene is indeed the most common one.
There's another video on YouTube of Mrs Incredible's head falling big off during a show on one of the cruises. Very awkward!