BFG ammunition pickups are square, yet the cells put in the weapon are round.
Mars' gravity is only 45% as strong as Earth's gravity, yet the Marine when outside of com-pressurized buildings walking on Mars's surface, is still walking on the ground as if there is no difference in strength of gravity.
Spelling mistakes in in-game text.
Some zombies are headless, yet when hey are gibbed the gibs contain a brain.
The word 'scandal' is misspelled 'scandle' in a newscast.
The suits worn by all characters are short sleeved, which would make them incapable of protecting the operator in a low-oxygen atmosphere.
Plasma cell pickups only yield 25 rounds, yet a plasma cell inserted into the plasma rifle has 50 rounds.
The ammunition storage cabinet near the Molecular Fuel Storage Compactor is behind the Compactor itself, which would hardly make sense since it would mean climbing over the Compactor in order to get to it.
Weapons eject shells from the left side of the weapon. Weapons are usually designed to eject shells from the right side of the weapon and away from the firer's face.
In the video disk video for the Molecular Fuel Storage Compactor, the text only says 'Union Aerospace' instead of 'Union Aerospace Corporation'.