Ok, that may explain it. POP stores all your mail in Users -> your name -> Library -> Mail and Mail downloads.
If you managed to have two accounts of the same name stored there, i.e. brought one over from a previous computer's migration assistant transfer, it would have trouble figuring which messages to delete.
Make sure you are only checking the message with one active POP account.
If you are, you might be running something that is corrupting your system. The Etrecheck in the link below can give you a report to share that can help us isolate what might be corrupting it:
https://discussions.apple.com/docs/DOC-250002463