I figured this out poking around in the directories and sorting out a little about how Mail works. Posting the solution in case someone else goes searching. Apparently this hasn't happened to many users.
In finder I opened the folder containing the mailbox folders of my POP account. It was...
When I go into Mail -> preferences -> Mailbox Behaviors and check the "move deleted messages to a separate folder" box, I get this message when I attempt to delete messages in my inbox:
The destination mailbox Deleted Messages email@usa.net does not allow messages to be moved to it...
