The scenes in which cows appear to be drowning or otherwise in danger were shot not with living cattle but instead with detailed model cows called "stuffies" or an animatronic cow.
Of course they're gonna get slaughtered. You think we'd have cattle if people didn't eat 'em everyday? They'd just be funny-lookin' animals in zoos. But we raise them for us. That means we owe them some respect. Nature is cruel, but we don't have to...
In the movie Temple's squeeze machine is thrown away but in reality it was put into storage.
There are photos of Temple Grandin (as a child, teenager and adult) shown beside the initial credits at the end.