Now that the freeze has turned into a crash (crashes are better they at least leave a crash dump file) I was able to hunt down the exact problem that was occurring and fix it.

The crash was happening when there was nowhere left to spawn Triggers or Structures because there were too many Cell type enemies around. This happened mostly in smaller levels and more on the hardest difficulty.

Now when spawning Triggers and Structures the AI will merely prefer spawning where there are no Cell type enemies and if it has to spawn over them they get destroyed so you can at least see where the Trigger is.

As part of this Hotfix when the Cubes trample a mutated Cell (the orange ones that explode) it won't cause it to explode preventing it from causing a chain reaction.