Revealing mistake: Have a look at the shot of the rear part of the train exploding as the locomotive pulls away from it. If there was ever a more obvious model shot, with cheesy, jerky bouncing toy trains and Action Man (TM) dolls, then I haven't seen it.
Plot hole: When the survivors first make an attempt to break out towards the station they kill numerous assailants at close quarters and yet only one of them (Uno) is infected. There must be dozens of the parasites floating around, enough to infect them all.
Continuity mistake: After Melanie's "plan A" failed since the train is not at the station the group fights its way back to the prison. During that fight they kill quite a lot of the possessed miners. But in one of the following scene when those freaks assemble in the streets and walk to the prison there are only four or five bodies lying around.
Continuity mistake: Early in the movie, when Ice Cube is accidentally released by the two rookie cops, Natasha Henstridge offers herself as a hostage to obtain the release of the blonde rookie. Ice cube switches hostages and holds a knife to Natasha's throat. Right as she slips out of his hold, the knife pushes against her neck and for a split second you see the blade bend.
Continuity mistake: According to Ballard at the beginning, a captain wears two bars (as per modern US insignia). However, Braddock wears two bars and her rank is given as Commander throughout the film.
Plot hole: When the Police first enter Shining Canyon, they make a point of mentioning why they don't have to wear a full breathing mask, because of the goggles they wear. (!) Later on however, several people who are not infected are not wearing the goggles, so they shouldn't be able to breathe.
Other mistake: When Dos is killed by his own grenade (after he dropped it) the direction the explosion sends him makes no sense. He should have been facing the other direction. (00:52:33)
Visible crew/equipment: When the team are retreating through the police station, as the infected invade, there is a moment where Ballard and Desolation place a heavy drum in front of a door to halt the advance and you can see the shadow of the camera at the bottom of the screen as it moves in. (01:10:52)