The following is just conjecture.
I know in the past I've seen settings (for IMAP email accounts at least) where you can map the client's Junk, Trash, Drafts folders to certain folders on the Server which might have slightly different names, like Spam or Deleted.
I would have chalked it up to Windows 10 Mail acting up and next time something goes awry, I would try to check the website if you have the option, because generally with email, the website/service/server has the last word on where your email is.