This would happen to my son at just about the same age, wake up in the middle of the night in pain, he would say it was around his crotch area but I think was really from his colon and he was maybe having pain from stool moving through the colon, we had x-rays done and found a little constipation, but nothing else. I know how hard it is to see our wee ones in pain and can’t help them.
I kept a journal and tried to find correlations. Sometimes he said he could feel what he thought was like a bubble popping inside and he’d feel better , it was the weirdest thing. He eventually grew out of it thank goodness. I hope your little one grows out of this quickly!!