iOS does not move mails to junk folder
I'm not at all sure this will work for you, but since nobody else has responded...

I set up a manual email account yesterday on both Mac and iOS, and my ISP warned me that both on Mac and on iPhone I needed to add "INBOX" as the IMAP Path Prefix in the Advanced Settings for the account, or else I would have trouble moving messages from Inbox to Trash and Junk. I was having a similar problem moving messages to Trash, and that did the trick. You might give it a try, since it's easy to undo if it doesn't work.