At the end of the first movie when Chucky is burnt, his left eye is there and his right is melted shut. But at the beginning of this movie, when they are cleaning him, his left eye is gone and his right eye is opened and there.
When Joanne is reading a bedtime story to Andy during the stormy night, she mistakenly changes her accent to her native English accent. She even makes a change in her facial expression making her realize of her mistake.
When Chucky is being reconstructed and when the other dolls are made, you an see their legs are hard plastic or rubber, like a G.I. Joe action figure. However various times throughout the movie, when the doll is moved, its legs hang limp and swing like a rag doll.
Andy's slippers disappear and reappear several times while he is tied to the bed.
Chucky's doll materials are not consistent. He is shown being made of plastic and his eyes are glass and movable, but when he is grabbed at some points in the point, his face is rubber, eyes painted on, and his "plastic" torso that was built in the beginning of the film is cotton.
The completed items in the shipping area of the factory at end of the film was arranged every which way. In a real factory items in a shipping area is generally stored making it accessible to pallet trucks, fork lifts and other devices, thus making it much easier to store and or retrieve such items.
For reasons unknown Andy and Kyle somehow were not caught on close circuit camera in the factory. The worker that died should had caught them at least and the pair would had been charged with trespassing.
For some reason, there is only one factory worker monitoring the production of the Good Guy dolls in the finale, as opposed to several.
When Kyle walks up the stairs you see a thread ball lying about halfway down the stairs. If a thread ball started rolling down the stairs, it would continue rolling to the bottom of the stairs.
When the toy makers are building the Chucky doll, they screw the battery cover onto Chucky. Later, when Andy inspects what he believes to be the Tommy doll, the battery cover does not have screws. If you watch in the beginning, when they actually put the batteries in Chucky, it is a plastic clasp door without screws. The screwed plate is seen above the battery chamber and is most likely the Good Guy doll's voice cassette, most likely screwed shut so children could not tamper with it.
During a commercial in the first film the Good Guy dolls appear at least partially animatronic. At the very least the head rotates, and the eyes and mouth move. However in the beginning, as the Chucky is being rebuilt, he appears somewhat less sophisticated. Being almost entirely plastic, and hard rubber.
When Andy opens the tap to the boiling, melted liquid plastic, some of the liquid squirts on his hand. The liquid is at boiling temperature and would burn him severely, but he doesn't notice, obviously because it isn't really boiling.
In the beginning of the movie when they are putting Chucky together, you see one of the Play Pals employees air brushing the freckles and eyebrows on Chucky's face but he didn't paint the eye lashes, he missed completely. Later on in the movie, you see that Chucky does in fact have those painted eye lashes even though they were never painted on.
When Joanne is kneeling by Phil's body, she cries, "Oh God no," and then, just before it cuts, Phil's right hand moves, even though he is dead.
When Mattson pulls the card through the card reader in order to open the door, there is no lock mechanism on the door anyway.
Chucky shouldn't be hard to beat since he's only a doll. The fact that Andy and Kyle aren't able to easily beat him doesn't make much sense.
Chucky had a perfect opportunity to process Andy in Grace's office after killing her especially how Kyle was locked outside. Likewise Chucky missed another chance when him and Andy were in the truck going to the factory.
Sound of metal against metal when Kyle takes knife from leather holder.
The sounds when Mattson is trying to fit Chucky in the boot are mixed up.
When Chucky first holds Mattson at gun point in the car he says "Don't move" but his lips don't move.
Reflected in a picture, as Joanne and Phil argue.
When Andy's foster parents are talking about Chucky and the camera slides from their room to Andy's, the camera is reflected in a few pictures on the wall.
At the end of the movie, when Chucky is remade in the toy machine, there is a hand visible as the credits roll.
Shadows in the garden, as Kyle is gardening.
After Andy knocks into something in the basement, in the next shot from behind, you can see a crewmember's head in the bottom-right of the screen, ducking down.
The film is supposed to be set in Chicago, however palm trees native to California can be seen looming in the background of the foster parents' neighborhood.
The Chicago Fire Dept fire truck is red but the real Chicago Fire Department colors are black over red.
There are presumably security cameras all over the factory when Andy and Kyle are running from Chucky. At least one of them should have captured footage of Chucky moving around, alive and sentient, proving that he is in fact alive.
How did Chucky manage to beat Andy to the Simpson house after they both left the school? Andy escaped first by climbing out the window, and Chucky didn't leave until after he was done killing Miss Kettlewell, but somehow got home first.
When Miss Kettlewell returns to her classroom she thinks Andy is in the closet but this is impossible as she locked the closet door so there was no way Andy could have got into the closet.
It is not clear how the murdered factory worker was suspended from the ceiling and left hanging. Chucky could not have had enough time to do this when he was shown chasing after Andy and Kyle all the time after the worker's murder, especially when he only had one functioning hand at this point.
How did the Play Pals toy company get ahold of Chucky's remains to rebuild him? They would have most certainly been locked up in an evidence locker after the events of the first film.
In the mirror, when Kyle bumps Joanne's dead body.
Andy would have easily been able to spit out the sock stuffed in his mouth. There is no tape holding it in and when Kyle enters the bedroom, she easily pulls the sock out with no trouble.
Miss Kettlewell locking Andy in the classroom all by himself violates several school rules and regulations, not to mention that it is a fireable offense, as leaving a student that young alone in a locked room is dangerous in case of a fire. The right thing for her to do in that situation would have been to take him to the principal's office to have his legal guardians called down to the school to deal with Andy. Even if Chucky hadn't killed her, she would have definitely gotten fired or suspended.
After Chucky failed to possess Andy at the factory he didn't seem to notice he's not possessed Andy until he began to bleed.
Miss Kettlewell saw Andy turn in his paper as she was collecting them from her students. She should have known that it wasn't Andy who wrote those profanities on that paper.