I have the same issue, but don't have a definitive answer as to why the crashing keeps happening. Are you working with a shapefile uploaded into your training sample manager from a previous session? That is where I have ran into problems. I have found through trial and error that ArcMap crashes when I try to merge a polygon with a class I had created in a previous session. However, I don't have any problems when I go to create a new class in an uploaded shapefile, and merge samples into the new class.
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