Having recently upgraded to the latest version of Remote Desktop for Mac, problems are reappearing that were resolved many years ago when we were able to liaise directly with the Microsoft Mac development team via HockeyApp, a situation sadly no longer possible.
There is a reoccurence of model type windows opening behind a foreground window. These are application built modal windows, not macOS system modal windows. This is particularly a problem when having an external display connected to a MacBook - seemingly a configuration rarely tested, despite being so commonly used.
The only solution is to continuously use the 'Assign To' each display and use 'Show All Windows' from the Dock, click on the modal window and eventually it will/may appear at the front so it can be closed. When the modal window is in the background it is not responding to any keyboard input, such as the 'Esc' key.
We've now reverted to Remote Desktop Version 10.9.6 (2188), which doesn't appear to be so badly affected, as the beta is now unusable to us. We've been using/testing the beta for 7 years now and it is disappointing to see old problems reoccurring.