don't allow multiple users with same email
Drupal by default does not allow multiple users with the same email if you try to create them through Drupal forms. If users are created by code this check is not performed.

My best guess it, that this caused by one of the rules Drupal commerce ships with. Specifically the "Create a new account for an anonymous order" rule. This rule fires when a user who is not logged-in completes checkout. It should check if the email is already registered, but might have been altered. 
Alternatively you might have a similar rule created yourself or by a module that does not check if the e-mail is already existing.

Most of Drupal commerce's behavior is controllable by rules, so I'd start looking there for rules that create users.