When Humphrey and Kate go to sneak aboard the truck, the bottom door is opened during Kate's failed attempt, yet a few moments later the bottom door is closed again with nobody having closed it.
When Kate and Humphrey land in the boxcar, both doors are open, but when the train is nearing Jasper Park, only one door is open; the one facing the park.
When Humphrey is water-skiing on the river while being pulled by Marcel, Kate is on the right bank. After Humphrey gets launched into the air and tries to use Marcel's wings to fly back to the ground, they land on the left side of the river. Kate appears right above them. She was on the other side of the river, and she doesn't appear to have swum.
In one shot shortly after Kate and Humphrey board the train, the view switches to a shot of the train as it crosses a bridge. In the span of about five seconds, it switches from day to night.
In the fight scene near the end, Kate is shown looking around for Humphrey. She has a flower in her hair, and when she turns around the flower is gone.