I know I was responsible for the precinct I worked being at least one provisional ballot out of ballot. Keep in mind, this was my "first day on the job" as it was for most workers. A woman came, wasn't in the book. Her English wasn't great, but she was asked if she had been sent here by the election commission to vote a provisional ballot. She said yes. I entered her name in the book. Then, when she was talking the inspector (who actually knew what she was doing) to go through the provisional ballot process, it appeared that she hadn't talked to the board, so she was going to call them and find out where to go. I didn't think to cross out the name, as I was busy processing other voters. So, it is likely appeared that she voted provisionally, but the ballot disappeared. By the time we were doing the midday count, there was disconnect between the signatures and the number of provisional ballots, but I had no recollection what her name was and wasn't going to risk removing someone's name from the book who had legally voted.
I'm betting shit like this happens all the time. In fact, in the training, when they talked about midday counts, they explicitly said don't worry if the counts are off by a few, but to sound the alarm if it's off by a bunch.