Throughout the film, Stubbins' hair changes very noticeably from neatly trimmed above the ears to quite shaggy, and back.
When Matthew and Tommy are dancing across the bridge during, "My Friend The Doctor", the 1st bridge changes to a different bridge when the shot changes to the opposite side of the creek and the fence that Matthew climbed over is no longer on the road but has changed to Tommy climbing over it at the 2nd bridge.
Dr. Dolittle escapes to the coast with a seal disguised as his grandmother. Soldiers stop their coach at a bridge. The coach in front of them crosses the same bridge three times.
During "Talk With the Animals" at night, no trees are outside the window. When the sun comes up, a tree's leaves are clearly visible.
"Sea Star Island" is a floating island with an active volcano. To be active, a volcano must be connected to a source of magma.
Blossom says he has been to Istanbul, but the city was called Constantinople until March 28, 1930.
The parrot says Jan, 30th 1649 was a Tuesday, it was actually a Saturday.
Due to coastal erosion, Sea Star Island almost certainly wouldn't fit perfectly back into the mainland after being detached for so long.
When the Flounder is first sailing, not only are the sails hanging limp, an obvious stirring behind the ship from its propeller indicates that it's being powered by an engine.
When Shelia the fox and her pups are shown, the baby foxes are clearly Chihuahua and Pomeranian puppies.
When the pushme-pullyu first appears on camera, there is an obvious split in the middle of its fur. The two sides are even a different color.
"Fabulous Places" contains a reference to Tasmania, which was called "Van Diemen's Land" until 1856.
Matthew Mugg plots to break Dr. Dolittle out of jail by blowing up the road with dynamite. The film is set in 1845, dynamite was invented in 1866.
In "I've Never Seen Anything Like It", Doctor Dolittle claims that the Pushmi-Pullyu climbed up and down Mt. Everest, which was not named until 1865.
Tokyo is listed among the cities Emma wants to visit in "Fabulous Places". Tokyo was called Edo until 1869; the film takes place in 1845.
When the dolphin retrieves the doctor's hat, the camera and crew are reflected in the water.
When Polynesia firsts teaches Dr Doolittle to say 'Good morning' to Gub-Gub the fishing line used to make her shake her leg is clearly visible over the Dr's right shoulder.
In opening credits, a bactrian camel, with two humps, is in front of the Egyptian pyramids. African and Middle Eastern camels are dromedaries, with one hump.
When considering ways to change the course of the island, Dr. Dolittle says elephants cannot swim. Elephants are excellent swimmers, which he should know.