This is because it is going off of User Name and Email not Role. Removing them as a Employee does not remove the notifications they are receiving as well. To change this navigate to
  1. onBoard > Settings > Notifications
  2. Select Online Application from the Category dropdown
  3. Click View, then click Edit next to the "New Account Created - Administration," "Online Application Submitted - Administration"  notifications
  4. Click on the Users name and remove from Recipient List
  5. Click Save & Exit.
This is the same process for any other Admin notifications that the User was enabled for. You would want to remove the User from the Notifications so they no longer receive them.