Pocahantas walked out on stage a couple of weeks ago, messed up the begining of the song, and walked back off stage and they restarted the show.
Seen many technical goofs in Fantasmic, most enjoyable was watching the princess boats run into each other (bumper boats!!!).
In the middle of the Playhouse Disney show, one of the (many) Jamies, mysteriously disappeared behind stage for quite a while while the show and audience sat quiet waiting. He finally reappeared and turned the page for the next part of the show and preceeded to mistep into one of the "holes" in the stage (where the puppeteers are working). It was quite an awkward and painful (to watch) fall, which he popped right back up from and continued off the front of the stage (like he suppose to do). I assume that he had a very loud call from nature....
Crush in Turtle Talk has to improvise a lot like when a kid takes the microphone (or won't give it back), or says something unusual...which makes this one of the best shows around (for what it is).
There was one Beauty and the Beast show where a dancer (must have) fell during the "Be our Guest" scene, and the show was stopped for about 10 minutes. They picked it up later in the show (next scene I believe).
Once, a dancer at Tarzan Rocks dropped his stick offstage right in front of me and almost killed me as he jumped down to get it as I was also reaching out to get it for him.
In general, though, considering how often we go to WDW and how many live shows we've seen, we've witness hardly any goofs to speak of...the rides break down far more often than the "humans" do.