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Two Puppies don't get along alone?

I have two puppies, one is a male mini dachshund a little over 8 months and a female “toy” australian shepherd that’s a little over 4 months. they get along great when i’m around. they play together, sometimes a little rough but nothing to worry about. they like to bite and and pin one another but they don’t show any signs of aggression when playing. they often do the initiate play bow.

recently however when they go to sleep or when i’m going to be gone longer then they can hold it i put them in their pin(a 36×36 elevated enclosed play pen) they have been getting into fights. as soon as i close the door to leave (or sleep) i can hear her growling and snapping at him and he starts crying. But as soon as I open the door they act as if nothing happened. I set up a camera just to make sure and she attacks him, backing him in a corner and snaps at him with her hackles up or she jumps on him and bats him in the eyes with her front paws while trying to bite his neck. It looks nothing like when they’re playing. He is submissive and all he does is cry.

They have been separated when they sleep now. I’ve never had this problem before. They have been living together since she was 9wks. I initially gave them separate living areas, toys, food bowls, etc. but they would only eat when they were together and they would interchange between one another’s dog bowls and would cry for one another at night.

now that i’ve separated them in two different pins across from one another she cries for him again and he refuses to even look in her direction and cries for me. And their barking and whining has been getting very loud. what should i do?

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