A GLA Hole would be left behind if a GLA building was destroyed. It is very helpful to survive one blast superweapons like Nuclear Bomb or MOAB (but not the Particle Cannon). From within the Hole a Worker could emerge to rebuild the building in question, at no cost to the GLA commander. The Worker that performed this task disappeared back into the Hole (and presumably the GLA Tunnel Network) after construction.
Enemy commanders had to be careful to eliminate the GLA Hole each time they destroyed a GLA structure, or the hard work of their troops would be undone. However, Holes are rather easily destroyed, not delaying a thorough attacker overmuch.
The GLA Hole also has an unused animation of the door opening, so the worker can go through and rebuild the building. Due to a programming error, this animation never actually plays, therefore the worker goes through the closed door.