Oh? I never had this bug. Except for one concerning an invincible carryall and commando
It would spaz out if you gave a "drop" command to a group, where some of them were over terrain where that was physically impossible. End result, you cannot select the transports that couldn't drop, and they just float there, looking stupid, doing nothing. I'm not sure if the AI could still target them, but I know I did
try to shoot them down myself just to get rid of the blasted things and it didn't work. (Found this is the GDI Croatia mission I think, killing the Banshee base.)
This was, however, fixed in a patch; I don't know which one, just that it was.