He may not like the bulk of the pull up at night since he is not wearing it during the day. Maybe he likes the freedom? Maybe he doesn't like feeling wet - but then of course he pees in the bed! What fun!
You could try putting the pull up on over his underwear but he will still feel very wet once he pees. Night=time training takes much longer. I would consider pajamas that he can't take off so he can't get the pull up off, as one of the other moms suggested.
My son had a bedwetting problem that lasted quite a while, so we made the bed by putting down a sheet, a waterproof crib pad (the size of a crib mattress surface but without going over the sides and being tucked in, followed by another sheet. Then when he wet the bed, we could pull off his clothes and the top layer, plus waterproof pad, and still have a dry sheet underneath. While that's not ideal, it saved us from having to completely strip and re-make the bed at 2 AM.
If your son has the same developmental issue as my son (and thousands of others), he may not be capable yet of waking up - the fact that he has a bm sometimes on top of the pee tells me that he may not have reached this stage. I would just put the pull up back on and tell him you want him to be able to sleep and not wake up wet - his sleep is more important than staying dry.
I have very mixed feelings about waking him up, dragging him to the bathroom, and making him pee before going back to bed. It really interrupts his sleep and it does nothing to get him to the developmental level he needs to stay dry all night.
In any case, it's important that he understand it's not a failure on his part if he "goes" at night - what's happening during sleep is beyond his control and nothing that can be "trained" - he just has to grow out of it. Good luck!