- That One Boss: Magnus at Mt. Weather, if he is hostile to you. He has an EMP aug that will disable rockets and grenades in his area, and can one shot kill you with his plasma gun. If he gets two other augmented soldiers to come out and help him, you'll also have to deal with them as well. The worst part is if you do manage to kill him, he explodes after death, and you can be very easily killed in the explosion.
- Unwinnable by Insanity: In Moscow, if you kill all of the major characters that can be killed and if you are shy of multitools before completing the Police Network mission, you'll get stuck, or if you kill major characters that can be killed and end up with not enough money to get into the nightclub.