It is possible to see that there are unread messages in the Account list / Accounts counter whilst you do not see any in the app. Aqua Mail takes the unread count directly from the server, i.e. the unread count of all mail in your mailbox. At the same time, the app does not sync the entirety of your mailbox unless configured to do so.

If you see unread messages but cannot find them in your folders in Aqua Mail, simply open up your mail provider's website and sort by unread. Your messages are likely old and not synced by the app.