You could also try having the radio on low and a night light, he is just a baby and may be lonely and scared on his own.
When we got our pup she was in a crate at night in our bedroom for the first 6 weeks until she knew her home and that we where only upstairs, we then moved her to the kitchen and she also took to that really well. She is now 8 months and we have now given her the run of the kitchen and the hall at night (beds in both with night lights on) and she is great - no problems at any time and no accidents in crates ever. Maybe being on his own is causing him anxiety and thats when he poos - I don,t know.

Hope you get it sorted soon, and he settles
Puppy Love

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And they called it.......Puppy Love xxx