Is this a Yahoo account?
First, there is a known issue (occasional) with Yahoo that sometimes their IMAP server reports as read messages that aren't actually read.
To check -- long press the account -> "Diag: message dates" -> choose Inbox -> run the test and you'll be prompted to send me a log file.
Second, if you use another mail app at the same time (desktop? Outlook?) and it's set up using POP3 -- then that will cause messages retrieved over POP3 to be marked as read in web mail and then sync as such (as read) into Aqua over IMAP.
Most if not all mail services will do that (mark as read messages retrieved over POP3), it's intentional and in any case it happens before AquaMail gets into the picture.
You can easily test this by not running your other mail app for some duration of time (and perhaps sending a couple of test messages during that time) and checking its settings to see if it's POP3 or IMAP.
If it's POP3, I very much recommend switching to IMAP there. It's much better than POP3 when you need to access your mail from several different mail apps / devices.