I had a client today who after every email they received in Apple Mail on Catalina, an error dialog box would pop up saying “The Message <whatever> could not be moved to the mailbox Inbox. Invalid base64 string for MIME content.”
After trawling the Apple support forums, where many people claimed to have done something that fixed it, only for the problem to reoccur minutes or hour later, what I did that seems to have fixed it was disable/delete the Rules in Apple Mail.
In particular, there was one rule in Mail that moved all messages from a particular sender to the Inbox – this was set up as emails from this sender occasionally went to Junk.
After deleting this rule, the issue has not surfaced again.