When Notes Migrator performs an AutoDiscover on the migration worker with Outlook 2016 installed, a certificate warning prompt is presented and the CMTProxy will not continue until the admin click 'Yes'. This does not happen to every worker, only a certain few.
This is an Outlook issue. You can work around this be adding the following registry entry on the worker machine and setting the value to 0
Data: 1 = Show certificate warnings/errors; 0 = Don't show certificate warnings
Contact Binary Tree Support at email@example.com if you have any issues with the above resolution.