Why are we assuming they were cruely treated?
One post talks about how this director was a huge naturalist and wouldn't harm animals, another how the bear is merely a cub (it pretty clearly is). If any animals died, it's probably due to the 4 year length of the film making.
Otherwise, some animals perform certain actions better the others, so I wouldn't be surprised if they used tons of pugs and tabbys to get the shots they wanted (one for swimming, one for sniffing, one for batting, etc.). Watch the scene in Day for Night where they're trying to get a cat to drink milk on screen if you don't believe me.
I like to believe a movie rumor as much as the next person, and I've dedicated tons of time to The Wizard of Oz hanging (not real, for the record). But I really don't think there are signs of any cruelty in this film (the waterfall and the bear batting at Otis are really not that bad to anyone who has ever seen a real cat fight or a cat jump out of a tree).