These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Soul Destroyers which are very hard to hit since they fly around.
Of course, giant spiders. They are so tough that the only way to kill them quickly is by using explosive weapons, but their favorite combat maneuver is jumping into close combat, so you have a hard time killing them without losing some of your own units to friendly fire.
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 and the viruses. For the love of GOD.
Nightmare Fuel: Every single virus. You thought mobile arrows weren't intimidating? Take a good look above and be proved wrong. EVERY SINGLE VIRUS has some hellish shrieking whenever you hurt them. Not only that, spiders are HORRIFYING in how they just jump on you.