Actually AA limits pets in cabins to 5 per flight in economy and you have to have an advance reservation--so it may take a long time to get them all on flights accompanied with people.
We probably will never have all the facts--but something went wrong in that cargo hold.
Puppies do not die from 85 degree heat at 6 am in the morning and were in the cargo hold in the air longer than on the ground and the entire time span is just a few hours.