Version 0.12.2 has been uploaded. This should resolve the issue... of newly spawned pentapods.
But you seem to have many of the big stompers now. They must be killed, to be replaced by the weaker pentapods.
As a suggestion, install my mod Planetary Peace, then enable Peaceful mode, this will kill all of the enemy units over a small period of time, the spawners will then spawn new units. Then click again after a bit, to return to hostile mode. You can then uninstall the mod if you like.
Edit: I just updated the mod, the animation is confirmation the active units were removed.