When Lisa flies her sled into the cake she gets cake on her dress, but after she starts walking away the stain disappears.
Mac and Zack's 'costume gloves' seem to fall down throughout the movie and reveal their skin color.
Throughout their escapades in Toyland, Lisa drives a pink car, Mary drives a blue car, and Georgie drives a purple car. Jack's car changes between pink and blue constantly. For example, at the Toymaster's Workshop he parks a pink car, then leaves in a blue one.
When the Toymaster shows Lisa the toy soldiers they are full of cobwebs and dust. Later in the movie when Lisa opens the door to the toy soldiers they are clean and shiny.
When Barnaby tells Justice Grimm to arrest the "little alien from the planet Cincinnati and that fat nincompoop", that is the only time he says "Cincinnati" as throughout the movie, Barnaby calls Lisa "Cinciwhatski".
At the beginning of the movie, in the toy store, "Jack" (Keanu Reeves) says "My Jeep's got four-wheel drive, I'll take you both home." But when Jack, Mary and Lisa leave the toy store, Jack is driving a Suzuki Samurai.
Towards the end of the film when the trolls are being pushed out of the gates, the troll in the middle-left has a hole in its mask showing the actor's face beneath.
A goose character in Toyland has a visible mesh screen on the neck so the actor wearing the costume can see.
At approximately 3:12, the mechanic knocks on the phone booth and says to Mrs. Piper "Ma'am we've put on your chains... Your chains." However, when he says "your chains" for the second time, his mouth does not move.
Starting at 1:07:09: When Jack is helping Mary and Lisa swing across on the rope, you can clearly see that the actor playing "Jack" alternates between Keanu Reeves and a stunt double. The stunt double's face can be seen the clearest at 1:07:12, and he also has a slightly different hairstyle.