This might sound strange, but do u think he could be doing it for attention? My son had ALLWAYS slept through the night, until our daughter arrived, he was 2 & half, and all of a sudden, whenever he stirred he would shout us! Until we went in. And then another couple times in the night. In the end, i explained to him that he cant do this as night time is for sleep ect, And i made sure he got as much attention as possible during the day so he wasnt feeling left out and in need of attention.
Just a thought! If he is not crying in pain or upset!