It can happen, because in code we seem to specify both User ID who did a checkout and billing e-mail from order.
However in versions before 5.2.x only 1 e-mail to billing e-mail was sent.
In 5.2.x we improved mailing system, but haven't changed the code, that uses it. This way 2 e-mail are sent out instead of 1.
Since billing e-mail is required field (not sure, but could be so), then I propose to:
- populate it with user's e-mail used during registration
- send e-mail only to billing address