Tbh I'm always kind of concerned whenever I see animals being hurt on screen and it's really realistic - I don't know much about filmmaking or training animals other than dogs, but seeing stuff like live horses that are clearly not props charging into battle and falling down/crashing to the ground, being stabbed, etc. always makes me uncomfortable because I'm not convinced that special effects or like really great horse acting can make it look so realistic.
But back on the topic of A Dog's Purpose, I don't understand what they mean by "it was deliberately edited"? Which part was edited? The dog was clearly resisting going in the water. And people say "oh but his tail was wagging, he must have been happy and just playing", but there's a lot of data that suggests a dog's wagging tail is only a means of communication and can convey many emotions besides happiness.
I honestly would not be surprised if this film (and others that use live animals) do abuse animals to some degree. There's only so much you can train an animal to do and at the end of the day, they don't understand "acting for a movie" the same way human actors do, so yeah, not surprised if some animals are forced to do things they don't want to on set.