In Terminator 2: Judgment Day (1991), John Connor is 10 years old, as we can see when the T-1000 looks up at the police car's computer. So the events in T-2 took place in 1995. As mentioned by John in this episode, 'that' happened 2 years ago, so this episode should be placed in 1997 instead of 1999.
When Sarah, John and Cameron go through the time vortex, they lose everything they were carrying - clothing, weaponry, and even bandages. Whilst Cameron's open wounds from battling Cromartie earlier in the episode are clearly visible, there is no sign of Sarah's gunshot wound to the shoulder.
In the information Agent Ellison is editing, Sarah Connor's height is listed as 5'4" and her race is listed as "Caucasian", and the mental facility Sarah escaped from is incorrectly spelled "rescadaro". However when we switch to the Terminator's computer, the bulletin, which otherwise contains the exact same information, lists her as 5'5" and her race is "White". The mental facility now also matches that of Terminator 2 - "Pescadero".
As Sarah watches the Terminator approaching in the opening sequence, the same truck passes behind him twice.
In the opening sequence when Sarah and John get arrested, Sarah is shown being forced into the police car from the passenger side. It then cuts to clip of the policeman pushing Sarah's head down into the car from the driver's side. Finally, it cuts to shot from inside the car showing Sarah entering from the passenger side.
A physical object of Cromartie's size and form would not be able to exert the thousands of foot-pounds of mechanical force needed to breach the door of a bank vault.
Near the beginning of the episode, Sarah Connor's FBI file is shown. It says she has a scar on her right shoulder, but she doesn't receive the wound that causes this scar until later in the episode.
After talking to John at his locker, Cameron passes a poster mentioning "guidence councilors." "Guidance" is misspelled. (The producers even point out the error in their DVD commentary.)
When the LAPD arrives at the bank, one of the cars says "Dedicated to serve" on the side of the door. LAPD cars' doors actually state "To protect and serve" there instead.
In the scene of Agent Ellison first meeting Charlie Dixon a wall clock can be seen on the wall several times, albeit briefly. Look closely and you can see that the clock isn't working, as the second hand doesn't move.
When her fiancé presents the ring, Sarah says John is 15 years old, moments later the FBI computers shows 16 as John's age. Possible explanation: the FBI computers calculate John's age by the year of his birth, hence he's technically 16 years old, but his 16th birthday is sometime after August 24th, so actually he's still 15 years old.
In the bedroom scene where John Connor is complaining about having been moved to a small town, he is listening to the song "Pardon Me" by Incubus on his CD Player. The song is the intro to the scene, which is cut off when his headphones are removed. This breaks continuity because it is supposed to be September 1999, and the "Incubus" album "Make Yourself," which the song was first featured on, did not come out until October of that year.
At the school parking lot, there is a Ford Focus parked outside. The scene is set in August 1999, the Focus wouldn't go on sale in the U.S. until later in the year.
When the classroom Terminator opens fire on John and shoots Cameron, she falls 'dead' before showing up later in the parking lot to pick up John. It makes no sense for Cameron to feign death in the classroom and leave John open to possibly being killed there when she couldn't know he would escape the Terminator and reach the parking lot.
When Cromartie walks up to the bank he determines that the S.W.A.T. team is no threat as they lower their weapons at the sight of him. From his appearance it would be understandable that they would be taken aback, since none of them know what they are really looking at. This doesn't explain why a moment later they don't act to stop him when Cromartie smashes through the doors into the bank, as this is what they are trained to do.