Today the problem occurred again, and I looked into exactly how it occurred.
The problem only occurs when I click reply on an email and then don't edit the email. After a minute or so, mail saves the email as a draft.
If I edit and send the email, or edit and delete the email, then mail will delete the draft.
However, if I don't edit the email and later close the email without sending it, the draft is not deleted.
I consider this a minor bug (though Apple should still put it on the bug list and fix it).
Here's the exact sequence.
1) select any received email
2) click on reply (the reply arrow works fine)
3) wait until mail saves a draft - do not edit the email
4) close the email (click the red button in the upper left corner)
the draft will remain in the draft folder. The dialog "Save this message as a draft?" will not appear.
Again, this is with a pop account.
And if I send the email, the draft is deleted.
I'd be curious to know if anyone else can repeat this problem (I'm using 10.12.13 on a macbook pro).