On trying to reproduce something else I have in my savegames and not sure how it happens (broken personnel slot buttons in Atlas base), I found a way that reliably makes the game crash.
Start new game
Place initial airbase anywhere
Click "Main Base"
Right click the workshop 4 times - this removes all 3 engineers and brings up the "Confirmation Required" window that asks if workshop should be demolished
With the window open, left click the workshop 3 times - this