I have seen this occur many times over the years, but didn't know what caused it.
I even had been haveing it occur in my single stage press. There, an occational case would refuse to slide out of the shell holder after deprimeing. I would stroke the ram again and every thing would be fine. And I thought for years that I wasn't getting the old primer out far enough.
Since then I found that some of my cases had primer pockets that were shaped oddly and would result in this.
A possible fix is to resize & deprime on the single stage press. The resizeing lessens the work that needs to be done by the progressive, also.
Or discard the cases that cause the problem.