Off the top of my head, I can't think of anything really significant that they screwed up - may need to go back and relisten to bootlegs of the shows I went to.
But one thing that was a super rare occasion that I did witness, which was similar to a noticeable mistake, altho caused by outside sources was the firemarshall show in LA on Feb 4, 2000. JL was held backstage, so MP fumbled the lyrics as best he could to TSCO and ultimately had the audience take over. I know a lot of fans were angry that they missed seeing the whole show, but being that I had tickets to the following night, it didn't bother me at all. And I cherished getting to see something completely bizarre and out of the norm - since when do you see police in riot gear creating a moving wall to force the audience to exit the venue?