It sounds like the problem happens after uploading a sketch to the Zumo 32U4. We have tested all of the example sketches for the Zumo 32U4 and have not heard of others having problems programming their Zumo 32U4 robots such that they are becoming increasingly unresponsive. As I said in my previous post, the Zumo can become unresponsive due to a bad program upload or when the upload is interrupted (e.g. USB connection is removed during programming). However, without any specific details, it is hard to pinpoint what might be causing the issue and fix it.
How often do the Zumos get in an unresponsive state?
When the problem happens again, I suggest having the students document their steps during the sketch upload (e.g. disconnected USB cable from Zumo unit before the Arduino IDE displayed "Done uploading") and saving a copy of that sketch file, even if it is an example from the Zumo 32U4 library. Then post those steps and sketch file here.