When I set up a pop account in Apple Mail ,it removed some of of my emails but not all.

I now get the following message every time i log into my hotmail account.

Your messages are in your POP folder!

Some other program is set to download and delete your messages from Outlook. Just in case this was an accident, we've put them in a special POP folder. Not an accident? Change settings

When i click "change settings", I get a message that there is a problem with hotmail right now.

I should note that in trying to fix the problem I moved my emails back to my inbox and deleted the POP folder . I also removed the hotmail account from the Apple Mail program .