> did you try simply removing the account and re-add it back but with IMAP settings, not POP?
Did you try my suggestion above? Just remove and readd account, make sure to IMAP. If this does not work, it means you have something wrong at outlook.com side.
Most likely, you have rules active at the server side. You may logon outlook.com via web (not your mail app) using your browser (such as Safari) to check the Outlook settings. Be aware, if you don't think you set any rules before and the rules are there, it is an indication of being hacked.
However, if you do prefer talking to Apple or Microsoft, I would recommend you to log on outlook.com first, check if everything looks good. If all are okay, e.g. you don't see duplicate emails in your Inbox of outlook.com using your browser, that means nothing is wrong with Microsoft, then you need to talk to Apple instead of Microsoft.
If you do see duplicate emails via web and you can't figure out any rules related, call Microsoft instead of Apple.
Does it make sense?