Had an interesting one happen today (playing on location at Pinball Wizard Arcade in Pelham, NH so I have no idea what version of the software was running).
It was actually 2 separate problems both involving minion mode around ghost boss battles. I wish I could remember every little detail of what happened as it happened but I'll just have to do my best to try and remember.
The first incident involved the Civil War ghost, the opening animation started up for it, the targets went up (I believe I had just started off minion mode by a random bounce but I'm not sure as it wasn't an intended shot, so it's possible a minion mode had just started a second earlier but I'm not sure), but anyway, the targets went up and instead of taking out the Civil War general's 3 soldiers, hitting the targets gave me the tones that it does when shooting the targets outside of a ghost boss to begin minion mode, and then a minion mode did start up, cancelling out the currently active Civil War ghost.
The 2nd incident I'm a bit more fuzzy on. I was in a 2 ball multiball after one of the ghost battles, I can't for the life of me remember which ghost battle it was (I know it wasn't the Prison ghost, it's possble it was the Hospital ghost but I'm not sure), but I was at the point where you're shooting the ghost for jackpots and the mode ended while I still had both balls in play. I then immediately scored 3 hits on the targets to start minion mode and lost one of my 2 balls in play. Play continued but it caused the minion mode to end, and the targets would no longer register any hits, the lights in front of them were all off and the lights in the ghost stayed off as well. It was ball 3 and the game didn't last much longer so I don't know if it would have eventually corrected itself or not. Starting another game afterward, everything was functioning fine again.
I wish I had a few more details on these incidents but it was hard to keep track of everything going on in the heat of a game and since it was on location I didn't exactly have the opportunity to try to repeat the bug.