Goofs

Early in the movie Alice directs her crew to heel to port. Visually, the ship heels to starboard.

The chess board (on both sides of the looking glass) is set up incorrectly, with a dark square at lower right rather than a light square.

As a child the Mad Hatter has his adult teeth but no gap between them. He also has no lisp. As an adult, the Mad Hatter has both a gap between his front teeth and a slight lisp. However, even in humans such changes can sometimes occur (e.g. due to injury), let alone in a weird magical being like the Hatter.

The princesses are depicted as having blue/green eyes as children, but with dark brown eyes as adults. However, the eye color can change over the years, under some specific conditions, even in humans, let alone in mysterious magical beings like Mirana and Iracebeth.

Alice lives in London, UK. The Wonder, her ship, has the American flag on it. However, many ships are registered in countries other than that in which the owner (or owning company) resides. This may be for tax or other reasons.

During the finale, shots show various areas of Wonderland covered in rust, frozen in time. One of these, using an earlier frame, is the White Queen's picnic table, featuring rusted versions of the White Queen, Bayard, the Hare and the Tweedles. However, all these characters, frozen in time, are at Time's Castle at this point.

Since Alice is using the Chronosphere to travel the Ocean of Time, she is witnessing different points of Underlands history, and not live events. Since the Time Rust is travelling through time, not just geographical location.

When the doctor attempts to give Alice a shot, he depresses the plunger to remove the air bubbles. In the following scenes, you can see that there is clearly a significant amount of air remaining in the syringe.