Apple Mail – Drafts folder synchronization
When using IMAP or Exchange accounts in several versions of Apple Mail, multiple copies of draft messages may be saved to the remote mail server in various stages of composition. Additionally, these messages may remain in the Drafts folder even after the message has been sent. These messages are not cleared after synchronizing with the mail server and must be manually deleted. There is no discernible pattern that triggers this issue, and does not occur with all messages.
Disabling the saving of draft messages on the remote mail server resolves the issue. Instead, these draft messages will be stored locally. This can be accomplished by unchecking the Store draft messages on the server option located in Mail > Preferences > Accounts > Mailbox Behaviors for each affected account.
An additional (optional) step is to create a folder in the remote mailbox and manually copy draft messages into it. Messages copied in this way will reliably synchronize with the mail server.