Please check if "Windows Outlook version 2013" is connecting to same account using POP3 -- and AquaMail is set up using IMAP.
As I wrote above, most if not all mail servers will mark as read, on the server, any messages fetched over POP3.
This is fine for POP3 itself -- it doesn't provide read/unread state sync, so a message's state is tracked by Outlook itself.
Trouble comes when AquaMail fetches same messages over IMAP a bit later (or already has them, and refreshes their states):
Since they're marked as read on the server (by having been fetched over POP3) -- and -- IMAP has read/unread state sync -- then this "marked read" state will sync into AquaMail.
To fix:
Switch AquaMail to POP3 or switch Outlook to IMAP. I think using IMAP everywhere is nicer.
To "switch", you will need to remove the account from the respective app and add it back, using Manual settings (in AquaMail), choosing the protocol (IMAP or POP3), and similar procedure in Outlook.