Hello,
Sounds like it's a POP3 account where the mail server shuffles the order of messages (relative to their dates).
If you can use IMAP, please do (you'll have to add the account into AquaMail again, in Manual setup mode, as IMAP).
If not, please long press the account, choose Options and Folders / Account options and increase the "messages to keep" setting. Ideally, you'd want it to be larger than the total number of messages on the server, but values above 250 or 500 might be impractical.