I couldn't find another thread about this specific situation, and it seems like a significant one. I just started an empty game by myself to get used to the game. Not even 3 minutes in my Commander paths into a bot factory and gets totally stuck. Here is a picture: http://puu.sh/3ows9.jpg It seems as if he wedged himself between the ramp and little column. He was shaking violently trying to get out. I tried giving him move commands and he was stuck for good. Maybe a collision box needs to be adjusted?
There's a bug in the current build causing units to path over structures, only way around it right now is to delete the factory if you get stuck. Hopefully it'll be fixed shortly.