This issue does not occur if users connect to the terminal servers using their public IPs or if they close the session and attempt to reconnect using the domain name.
This is how they end up with two sessions, one on each terminal server. Upon entering their login credentials, users are logged on the other server. Unfortunately, MRD often seems to fail to 'negotiate credentials' as it lands users on the login page. Upon waking up from sleep, MRD attempts to reconnect to the terminal server. The issue occurs if a user's Macbook goes to sleep.
This issue only occurs for users that are connecting from Macbooks - they are using Microsoft Remote Desktop for Mac.