Darwinia/YMMV

Demonic Spiders: Soul Destroyers which are very hard to hit since they fly around.
Game Breaker: Engineers can move anywhere, and capture Control Towers as long as they remain unmolested long enough. And resetting a level doesn't reset the Towers. This means distracting higher-level monsters, such as Soul Destroyers, with a Squad while your Engie captures a tower is a viable strategy.
- Progress toward capturing a tower is also not lost, which means if the Engineers get even a tiny bit of work in before buying it, you'll get the tower eventually. And the tower only has to be 50% captured for you to start spawning Engineers or even Squads in atop it.
Goddamned Bats: Spore Generators due to their ability to float out of danger after getting hit, Triffids because many of them are placed on remote locations and Army Ants for their multiplication properties.
Good Bad Bugs: When you save a level, the save is not an exact state save, and glitches can occur as a result. On the Yard level specifically, the existence of individual ants is not recorded, only the anthills that spawn them. Thus the requirement to destroy all ants (as opposed to all anthills) on the level can be met as trivially as exiting and re-entering the level.
Hell Is That Noise: The screams of burning Darwinians.