When Timmy is older, and singing I will show the world, a scene transitions using flowers, some of the flowers aren't colored, while others are.
After Timmy meets Mr. Ages, a chalkboard is shown, which has a math problem done incorrectly. 9 times 27 equals 243, which would result in a remainder of negative 20. Remainders shouldn't be negative. The correct answer is 18 remainder 7, which equals 18 and 7/27.
When Mr. Ages tells Timmy that the valley is safe and remains unknown to the world, how can Thorn Valley be safe from being found when it's obvious that the city built above ground can be clearly seen by anyone from the sky. Also why didn't the mice build their city underground or camouflage their buildings with grass roofs, or have their homes built in trees, any human would've found their city by flying over in an airplane or helicopter and they would've been in big trouble with humans.
When one of the forest animals gives Cecil a credit card, how is it possible for them to pay Jeremy and Cecil when there's no credit card machine to pay with. The credit card would've been useless since the forest animals have no access to a credit card machine and they would've had to go to a nearby town to use it.
When Timmy first receives the key to the city it fits in both his hands, late when he's older and he uses the key to escape it only fits in one hand and is much bigger.
At the end Martin says Tim saved Thorn Valley single handed, however, he had clear help from Cecil.
Some of the character's mouths don't sync well with the dialogue.
Throughout the entire movie, characters mention that Nicodemus foretold the prophecy. He said nothing about the prophecy in the first movie.