Can happen if you mix IMAP (in Aqua Mail) with POP3 (in another mail app, say Outlook for Windows).
POP3 has no support for marking messages as read or unread. Some mail services mark messages as read once they’ve been downloaded by a mail application, some do not.
IMAP does have support for syncing the read/unread per-message state.
So what can happens is:
– a new message arrives, is initially unread;
– when it’s retrieved with Outlook for Windows (let’s say) over POP3, the mail service will mark the message as read;
– since POP3 has no read/unread sync, the message will remain unread in Outlook;
– but since it’ll be marked read on the mail server, and IMAP (in Aqua Mail) does have read/unread sync, the message will show as read in Aqua Mail.
Solution: don’t mix POP3 and IMAP. The best way to access an account from multiple email apps is to use IMAP in all of them.