I'm no expert (but) have a suggestion...
Do they keep the crate in their bedroom? I've heard the majority of pups will whimper a bit before they need to go poop. Kate did when she was being house trained, and my friends' pup still does now at 9 mnths of age. If the crate isn't being kept in their room at night - I'd suggest starting with that. When the pup whines in the middle of the night - take him out and praise him like crazy when he poops!
Another thing they may be able to do (on a weekend or something) is to stay up for a night or two with the pup (and sleep during the day). I know it's a sucky thing to have to do (but) if they're up, the pup may ask to go out when he has to poop. OR - when he starts to poop then they could take him outside "mid-poop" to show him he's not to poop in his crate...
I've heard of a lot of dogs that poop in their crate instead of waking their owners during the night. I'm guessing it's because they realize when their owners are in bed - it's time for me to be quiet too. Maybe the pup just doesn't want to wake them up?
I hope it works out for them...