I had the same problem with a pup I bred, I kept a pup back out of a litter. For the first 8/10 weeks my bitch couldn't have been better with her pups, but after that she hated the pup that I kept back and I mean hated, I couldn't let her near the pup ! I kept them apart and slowly introduced them to each other again. Now my pup is 13 months old. The pup and her mum are now best of friends.