I've had similar things with all my kids. My middle one is very prone to nightmares. She's just a sensitive worrier. My oldest does something like you describe. When she is deep in sleep she will sometime wake up crying, but not be coherent. It's almost like she's sleep walking. It's always because she has to go to the bathroom. She weeps through the entire trip to and from the bathroom, but instantly falls asleep when I lay her back down. If I try to ask her what's wrong or talk to her while she's like this, she responds mostly with gibberish.
Might your son be deep in sleep but can't wake up enough to get himself to the bathroom?