My 15 week old Bullmastiff is pooping in his crate at night and then eating his poop. He did really well the first 2 weeks, but over the last week and a half he has had 4 accidents. We take him out between 10 - 10:30pm every night and sometimes he has a bm, sometimes he doesn't. Then I get up with him again at 2:30am and have had luck sometimes getting him to have a bm, but sometimes he just won't go. At 5:15am I then find evidence of an accident. He is really good during the day when he is crated and hasn't had an accident in the house for 3 weeks. He even goes by the back door to tell us he needs to go out. It is just overnight that he does this. Please help us!

Maybe you need to look at his diet. There may be some deficiency that he's trying to make up for. Sometimes they do lapse as puppies but patience and consistency is the key. Make sure you heap LOTS of praise on him and make a huge fuss when he does a bm outside (which you probably do already.)
He may just like the taste of it and knows there's no one round at night to stop him from having his wee treat lol. On the other hand I've heard that some dogs are very fussy and try to clean up their area, especially if they're in a confined space, but I don't know if this applies so much to a puppy.

I agree with moparbyfar... dogs usually eat their own poop when they're lacking something in their nutrition. Are they on a puppy chow diet?

Are you feeding the dog enough?

Sometimes, the stress and anxiety of being alone in the crate can lead to eating his poop. Is it crate trained properly?

Try putting a little bit of pineapple juice in their food... as it will make the poop taste horrendous.