- Anti-Climax Boss: In the PC version, the final opponent is Doyle, a weak scientist armed with a P90 and hiding in a control room. He goes down in one shot. Then again, at the beginning of the final level, you fight Big Bad Climax Boss Mutated Krieger, who puts up a much bigger fight.
- ...And he's not much of a threat either, if you fight him by getting in close like you fought all the other giant trigens.
- Alternatively, you can just shoot him in the crotch, as he takes massive damage if hit there (who doesn't?) and goes down after only a handful of bullets.
- Demonic Spiders:
- The monkey Trigens. Since the shotgun has little to no stopping power against them, if they start their leaping attack and aren't dead by the time they reach you, you can wave goodbye to half your health.
- In Instincts, there are Kamikaze Trigens, who run at you screaming at the top of their lungs and blow up in your face, killing you.
- Narm: Jack. Daaaaar, Doy-ul?
- Porting Disaster: Vengeance is widely agreed to be one of these. Even the future Angry Video Game Nerd does a review on the game in the Present Nerd's Nightmare Sequence in Yet Another Christmas Carol. Ironically for a Wii port, the motion controls are actually regarded to be very good by most players, but everything else seems to have come up short.
- Scrappy Level: When you get booted out of a helicopter, with an almost empty gun, into a jungle chock full of Trigens. With one charging at you right at the beginning.
- The Scrappy:
WHAT ABOUT THE WHALES, GEORGE?
- "Food guy" Emillio for being an unfunny comic relief.
- The tourists looking for whales, as they are an another case of annoying comic relief.
- Plot Tumor: The Detective Cordonís investigation of Heatherís death. Itís not badly written per se, but it goes on for too long, with little progress or significant character development. The eventual revelation that Lee was partly complicit in her death and was responsible for covering it up just doesnít elicit much emotion.
- Unintentionally Unsympathetic: Will Grayson. His superior makes a very good point that his obsession with Mitchell Roberts is destructive and the methods he used to gather evidence were deeply unethical. Sadly, once Roberts escapes, he is treated as being right all along in his methods and he never gets confronted by either Christine Fell or someone else.