In the woods the mother dog gets picked up and put in a bag, then a second later the group of dogs come to a halt to see this and the mother dog is there in the group.
At one point in the museum, Cooler's black nose completely disappears.
In the opening of the film that dad dog is again telling his daughter puppy about another part of history and when he is done he refers to the "kids" listening to the story, but she's the only puppy there.