What to do when Cysts stop connecting?

I just played a game where the commander couldn't drop any more cysts and the ones already in the game wouldn't connect to any hive.
Of course, this turned around the whole game and coincidentaly happened just after alien team got the upper hand and begann to "boom" their biomass.

Needless to say the game crumbled like a bridge made of ritz during rain while the remaining cysts popped like crackers.