Have you checked with the Email Log plugin if WPERP fired 3 emails or it just two?
Matt, you probably know what bug is. An intentional feature could not be a bug actually 🙂
No, we do not offer approving leave by a supervisor at this moment. Only HR managers are responsible for that. So, as we do not offer this, this is not a bug anyway. However, we have the plan to bring the multi-step leave approval feature in the near future. Supervisors and Managers, both will be allowed to approved the leave request.