Despite taking place immediately after Half Life 2: Episode 1, Dr. Freeman's hazard suit has an upgraded flashlight with an independent power supply, which wasn't seen in Half Life 2: Episode 1.
Valves sometimes turn to the left to close, even though the standard is to turn to the right to close.
Grammar mistakes in subtitles.
The ammunition for each weapon should be a multiple of the maximum ammunition that can be held within a magazine.
The ammunition icon for the MP7 submachine gun is that of rifle ammunition. In reality the MP7 submachine gun fires 9mm pistol ammunition.
The drums marked 'Flammable' are explosive and not flammable.
Weapons sometimes reload themselves if unequipped.
A printer at the White Forest base is printing so fast that the paper should be jamming.
The evens within the game take place in Eastern Europe. In some parts, a chickadee can be heard. Chickadees are only found in the Americas.
For some reason, killing the Guardian renders the larval extract useless even though the Guardian is never even in contact with the larval extract.