Okay so the other day my son had his girlfriend over and I have never left him alone whit a girl before but I had to run to the store to buy some flour I told him I wouldn't be longer than 20 minutes and he said okay so I left and about half way to the store I couldn't find my credit card so I turned around to go get it and I walked in the door and went to find my credit card when I heard a small Mon and then my sons voice "its okay" I walked over by his room and the door was craked open and I peeked in and saw him thrusting into the girl I called his name and he looked at me and shouted to shut the door I did and waited for him to come out and he hasn't do I confront him? What do I tell him? Should I punish him?
Don't do anything until you've had time to process what you saw and decide how to deal with it.
I don't think punishing him is the answer. You can do better than that - use this time to educate him. It is past time to have a talk with him about sex - really in depth, including STD's, pregnancy risks, masturbation, and birth control. Don't leave anything out. Encourage him to ask questions and answer them - exactly.
Unfortunately many teens rush into having sex. Their bodies are ready, physcially, but not their minds.
Remind him that sex is something special to be shared by couples that have a commitement to one another.
No doubt he's very embarrassed by what happened. Use that to your advantage.
Then make sure he understands, no girls in his room.