This is occurring because it is going off of User Name and Email  that is listed on the Notifications list and not the Role. Removing the Role as a Employee does not remove the notifications they are receiving as well.

To change this navigate to:
  1. Enrollment Management > Communication > Notifications
  2. Click the Notifications tab
  3. Select Online Application from the Category drop-down
  4. Click View, then click Edit next to the "New Account Created - Administration," "Online Application Submitted - Administration"  notifications
  5. Click on the Users name and remove from Recipient List
  6. 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.