Dog with separation anxiety pooping at night

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Hi guys! First of all, I want to apologize for formatting because I'm on mobile. All right, here goes.

So, I've got a complicated situation with my puppy. He's a 10 month old CavaPoo (cavalier King Charles spaniel and poodle) and house trained for the most part. However, he started pooping in our room in the middle of the night, without waking us up to take him out.

He sleeps in bed with us and not his crate because of his separation anxiety. He'll cry really loud and we don't want him to be upset or to keep our apartment neighbors up. We're working on crate training but it's a slow process.

One other complication is that he poops right before bed when we take him out, and we put his food away after he poops. So I'm not sure how he still has poop in his system during the night.

The final complication is that he basically free feeds, a habit formed from his previous owner. We are working on getting him on a feeding schedule but it is slow moving, and he only eats a little bit at a time. I'm not sure how this could affect the pooping issue though, since like I said we put his food up after he poops in the evening.

Miscellaneous info: he poops twice a day, once in the morning (or in the middle of the night) and once in the evening. He usually poops around 10 pm, and then we take him out again before bed at 12, but he only pees then. We go to bed at around 12 and wake up around 8.

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