Minor Plot hole: Sarah Connor's confinement cell features the most advanced security measures to keep her locked-in – but somehow, the contractors forgot one big detail. You know what is the first step to keep your mental institution's inmates inside? Make sure doors are not installed backwards by drunk union workers where the keyholes are displayed from the inside of the cell – otherwise they can be lock-picked. This is why it never happens ever. Except in this movie.
Minor Plot hole: The Austrian terminator mentions that the T-1000 can copy any human he personally touches. This is shown to be accurate for the whole film with the exception of the mental institution guard who only touched the T-1000 with his shoe before transforming. Unless the prison guard is a deviant who regularly masturbates on his own footwear, the soles that the T-1000 touched would not carry his genetic code.
Minor Plot hole: Early on in the film, it is confirmed in a giant plot-twist that Dr. Silberman who is in charge of running a mental institution is also himself a retard when he agrees with Sarah Connor that she has been really nice for the past 6 months even if it was only weeks ago that she stabbed him in the kneecaps with a pen.
Major Plot hole: The movie ends with all traces of Terminators extinguished from the present. The T-1000, the T-101 and the old parts of the original Terminator where all thrown in the molten metal pit. Hmmmm. Somehow – something seems to be missing. Could it be Arnold's detached robotic arm? Oops.
The fact that they all forgot the arm could justify the original premise that there is no fate and simply a circular history that is inevitable. Nonetheless, it makes no sense for any of them – and especially Arnold to not think about fetching his arm he forgot in the gears a few meters away.
Plot Contrivance: The T-1000 is not very imaginative when it comes to finding the fastest ways to kill his targets. While he was on top of the elevator slowly and blindly trying to slash the Connor Family with his liquid metal swords – he forgot to realize he was on top of an elevator, with aforementioned liquid metal swords beside elevator cables that sustained the elevator from falling down to mortal velocities in the basement.
Unaddressed Issue: Why would the T-1000 appear naked in the present (1991) with human skin? It would make more sense to see him in his original metal color state. Was it to not sell the punchline too quickly ?