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Some dogs do whimper when they are doing that.. Or it could be because something is biting him like flees or something.. Just take him to the vet... Could be a lot of reasons honestly.. Like the kind of the food you give him just call an animals clinic and let them know whats happening and they should be able to help you over the phone.
he may have eaten something he can not pass. you may want to take him to a vet to get checked out, this is not normal. his anal glands may need to be expressed.
It's a sacred ritual. I do it too, lol. Your dog and I share a bond. Lifelong. We find it absolutely thrilling to howl as we sh*t.
It might be hurting him? You should get him checked if your concerned.