I've only had 2 issues like this.
Once, when AA still through checked to other PNRs, I was in BOS heading though JFK and on to the west coast. 2 PNRs, checked through fine. Boarding passes issued.
While I was in the lounge, someone removed me from the BOS-JFK flight and when I went to board, the reader beeped. Got it fixed, but lost my front row economy seat and was bumped back to the exit row.
The other was in LHR, flying to China with their Transit without Visa scheme. All documentation was fine, just the check in staff had no idea about the Chinese TWOV system. 20 minutes and a number of phone calls later, and I was checked in and everything good.
Only when I went to board, I found someone had removed the DOCS OK flag from the system and had to go through the entire TWOV verification process again.