My son is 26 weeks old and used to do the same thing you are describing...
My first answer is similar to all the other mommies... Your little one cannot talk yet and can only cry to let you know what they need. Even if it's 3 AM, if feeding him helps him calm down, maybe he was just hungry. Some babies can't sleep through the night without a little help. That's just something you'll have to expect for a while.
As far as the rolling to the stomach: as long as your baby is rolling himself, and has enough head control to keep his face out of the matress, you should be fine. It's never okay to put a baby to sleep on their stomach, but babies sleep in all kinds of weird positions. My son sleeps on his knees and elbows... and he has since he was 2 months old. I put him to sleep on his back and he will roll over right away. If I tried to fight that and continue to roll him back to his back, it would be an all night fight.
Good luck! Hopefully things will calm down and allow you to get some sleep through the night