The issue MDL-64017 added a message digest which is the cause of this issue.

The scenario.

1. The messaging email processor is enabled.
2. User A sends user B a message.
3. This gets added to the message_email_messages table.
4. User B then logs in and reads the message.
5. The task message_email\task\send_email_task is run and sends the message (that has already been read) to user B.

We can avoid this by removing the message from the message_email_messages table once it has been read.