Sometimes I work on a message in Apple Mail, and temporarily save it to my Drafts folder. When I open it again, finish it, then send it, occasionally it stays in my Drafts even though I can see that it was Sent. I can manually delete it, but there’s got to be a better way.
Go to the Mail menu and choose Preferences. Click on the Accounts button at the top. Click on the email account that has the issue. In the right pane, click on the Mailbox Behaviors tab.
Is there a checkmark in front of “Store Drafts messages on the server”? If so, uncheck it. From then on, drafts will only be saved on your computer, and not on your iPhone or iPad…but they won’t get stuck in your Drafts folder anymore!
Repeat this step for all other IMAP accounts you may have.
(Note that this option has been removed as of OS 10.12 Sierra).