During "Trainyard Blues," Chugs rotates on a turntable which is smaller than his body.
Early in the film, the Mailman is seen as one of the child founders of Kidville. At the end, he drives some of the other founders on his train, and he's now an adult while they remain children.
A number of Easters are celebrated, yet the children of Kidville remain the same age throughout all the years.
Gadzooks bars Sunny, Linda, and Herbert from crossing Big Rock Mountain, throwing Sunny's basket of eggs across the treetops. He doesn't touch the baskets of Linda and Herbert, yet all three return home empty-handed.
During the makeover of Gadzooks, Mr. Jones tells him to take off his shoes so he can feel the sand in his toes. But he never wore shoes (or any clothing) until this scene, so giving him shoes in the first place was counter-productive.