Why are there flagged emails that I don't flag?

Try this. I had the same problem for over a year. Check to see where all the flagged emails are coming from ( meaning which email address of yours are they sending the emails to ). Mine was coming from my Hotmail account and would always end up in the flagged section of apple’s email platform.

Now when you open apple’s email platform where your emails are synced , check to see if you have 2 junk folders for one account. I noticed that my hotmail account had 2 junk folders ; one that came with hotmail and one that looked like it was created ( it had a folder icon.). I erased that junk folder. Let me know if that does the trick for you. I did some other things after that but I think that will work. If it doesn’t let me know and I will tell you what else I did. But it’s been 2 weeks now and I haven’t received anymore unwanted flagged emails to my account.

If someone sent you a message and flagged it before sending, it will come there.

Filter emails in Mail on iPhone - Apple Support

If the filter is turned on your phone to see just flagged messages, it will group the flagged messages first. Undo the filter selection if you just want to see the messages by some other sorting category.

This is where it is useful to set rules in Mail. Note they only apply after you manually select Apply rules on all selected messages. Mail menu -> Preferences lets you create rules.