When I put my dog (who is a 12 week old lab) in his cage for the night he continues to poop and pee in the cage. He does this even thought I let him out before bedtime. When I wake up in the morning to take him outside he is laying in it. My cage is huge you would think he would lay on the other side of the cage, but no.
My husband raises/trains coonhounds. At times, there will be one that will pee and poo in their sleeping house in the kennel. He will put their food and water bowls there in the house(for your uses, the crate). They usually get the idea to not use the bathroom when that is the only place they can get food and water.
It could also be that your crate is too big for the puppy. He should only have enough room to lay down. To avoid having to buy another crate, see if you can get some plastic canvas or anything else to make a temp divider until he is big enough to fill up the whole crate. If they have enough room, they will use the bathroom in one end, and sleep on the other.
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