In the last scene where the male bug is struck by the train, you see it struggling to hold onto the front of the train for a while. It manages to hang in there for a little while before being pulled under and splattered everywhere. But when Dr Susan looks around the corner, after the bug is killed, she sees parts of the bug just meters away from where she was hiding. The bug should be further down the tracks, because it was dragged for ages before going under.
The news report about the Judas breed claims that roaches are "infected by an enzyme" when they touch its secretions. Enzymes are chemicals, not pathogens, hence can't "infect" anything.
Near the end when Dr. Peter Mann is running from the female Mimics, he does end up in the larva room and gets the idea using his lighter and the gas to neutralize the upcoming threat with fire. When his Lighter does not function anymore and he loses it in the water he gets the idea to use sparks created by the pickaxe, which worked quite easily. However whilst all the gas pipes were metal and you hear the sound of metal hitting metal, there happened to be no single spark while he hit a dozen holes in them.
Termites have kings and queens, but the giant mantis/termite hybrids seem to have the former without the benefit of the latter.
Insects cannot grow as large as humans, their body structure just doesn't work at that size. Though they apparently evolved lungs, it doesn't get around the molting problems or lack of an efficient vascular system in a bug that size.
In an aerial stock shot at around 9:00 min running time of the Director's Cut, the PanAm Building is seen. It was re-branded MetLife Building in 1993, when in fact the film is set in 1997.
When Susan goes into the abandoned subway office looking for Manny, she calls out "Chuy?" and not "Manny?" Chuy is hiding in the office, but at that point in the film she doesn't know it yet; she has no reason to expect to encounter Chuy and no reason to call his name. In fact, as far as we know, she shouldn't even know his name.
When Susan (Mira Sorvino) takes her pregnancy test, she and Peter (Jeremy Northam) move around and shake the test. This often results in false readings.
Dr. Susan states that if they kill the Judas Breed king, the whole species will die out because the single fertile male will be gone. However, this completely ignores population dynamics, operating on the baseless assumption there's only one colony of Judas Breed in the whole city when there should've been many colonies already (which could explain how there are sequels).