Tik-Tok's thinking mechanism is activated by winding the key under his left arm, and his talking is activated by winding the one under his right arm. However, when he asks Dorothy to wind his thinking key before entering the ornament room, she winds the one under his right arm.
Jack Pumpkinhead's neck thickness varies throughout the film, it constantly goes from the thin stalk-like neck (puppet) to a thicker, shorter, more normal neck (actor in a suit).
The Lead Wheeler's eye make-up changes between scenes.
When Dorothy and Billina stand and talk in the chicken coop, in some close-ups there is a piece of something like plywood in front of them that is not there in longer shots. It is probably used to conceal Billina's puppeteer.
When Tik-Tok lands on the Nome King's mountain, the amount of him sticking out of the sand changes between shots.
Most discontinuities between this film and The Wizard of Oz (1939) cannot be considered goofs. Director Walter Murch stated that this film is more of a homage than an actual sequel.
When Dorothy asks Jack where Mombi got her 30 heads, he tells her they came from the headless dancing statues in the Emerald City. There were only six dancing women that Dorothy saw. However, she only saw a small part of the city so it's possible there were more; this was simply not clarified.
The melting point of silver is 961.78°C, or 1763.2°F. Its boiling point is 2162°C, or 3924°F. Therefore, Dorothy would not have been able to drink "hot liquid silver", or even hold the cup for that matter. However, this scene takes place in a fantasy world where chemistry is different than in ours, e.g. tin can rust.
When interrogating the lead wheeler, Tik-Tok claims that being a machine he cannot be sorry or happy; yet at the Nome king's mountain he sheds tears suggesting he is capable of emotion. This is meant to be a character arc, showing that he is maturing and discovering previously unknown attributes.
The nurse unexpectedly takes away Dorothy's lunch pail. Yet before she even reaches for it, Dorothy raises it up, as if handing it to her.
At one point Dorothy bumps into the "stone" Cowardly Lion and it wobbles back and forth.
The strings for the harness when Dorothy fell onto the piece of furniture when the crew arrived at the Nome King's Mountain.
When Mombi wakes up and walks around headless, it is obvious by her stiff jerky movements, and the way she glides rather than walks, that is an animatronic puppet and not an actress.
When Dorothy and her friend run away from the hospital in 1899, Nurse Wilson chases them with a flash light, invented in 1902.
At the very end, there is a teddy bear on Dorothy's dresser. The movie takes place in 1899, but the teddy bear was not invented until 1903.
When the other girl is unstrapping Dorothy, a close-up shows her saying "We've got to get you out of here." When the camera pans out, it shows her mouthing the exact same line.
When Dorothy steals Mombi's ruby key, a headless Mombi is heard snoring; snoring occurs from the flow of air causing the soft palette at the back of the throat to vibrate, therefore without a head, Mombi would not snore.
When Dorothy first meets Tik-Tok, he tells her that he will be her humble servant, takes off his hat and bows before her. When he's bowing if you look closely you can see the "puppeteer" crouched behind him.
Uncle Henry tells Em and Dorothy to back by dark. This is impossible, as Franklin, Kansas is 163 miles one way to Cottonwood Falls, 326 miles round trip. There was no vehicle in 1899 that could have made the journey before sundown.
The lair of the Nome King is seen from the tower of the Emerald City from around 10 miles away or so but it seems to take all night for Dorothy and her friends to get there. It should have taken around an hour at most to get there.
Mombi sends the Wheelers to hunt down the flying Gump. This makes no sense, as the Wheelers cannot fly, and have no anti-aircraft weapons.
In October 1899, Doctor Worley says that it will soon be 1 January 1900, and a new century. This is a popular misconception. Mathematically, the transition between centuries happens in 00/01 years, not 99/00 years. Also, he states it will be a new year in two months, but the mystery girl claims "it's Halloween soon," meaning the story takes place no later than late October. Two months after this would be late December of the same year.