Are they same old messages over and over again?
Do you use a desktop mail app to delete some (many? older? newer?) messages from the mail server?
Do you accumulate a lot (dozens or more) messages in the Deleted folder in AquaMail, without emptying it?
It would help to know if it's POP3 or IMAP.
But either way, please long press the account (in the account list, app's main window) -> "Diag: message dates" -> choose Inbox (if offered), run the test, and you'll be prompted to send me a debug log. I'm at kmansoft / gmail.