* DemonicSpiders: The mutant in levels 1-3. It constantly tries to jump on you, causing an instant kill if it succeeds, or at least destroying any vehicle you're using. This is used as incentive to prevent harvesters from eating too many humans so that the mutant never appears. In contrast, the level 4 mutant has a better weapon, but is less of a threat because it hovers instead of jumping.
** The stationary Alien Gunners in Java are no slouch either.
* FridgeLogic: The aliens cloned The Man In Black from a drop of Adam Drake's blood, which they are shown to acquire in the opening video, set in 2016. The Man In Black then leads the aliens' ground forces in past eras. The aliens are never shown to possess the same time travel abilities that the humans do, so how did The Man In Black even exist before the aliens found the blood?
** Reverse genetic memory?
* NightmareFuel: Get scooped up by one of the people snatching green blobs during a harvester wave and you lose all control of Adam. Watch as he's brought towards the jaws of the harvester, and consumed alive.