I'm sorry but what?

I'm guessing you mean that his throw beat your charge. That isn't possible unless you started your charge from so far away that it wouldn't have hit him.

nope it was a wake up shoulder charge, and i was really really really close, like probably i'd say touching or really close, i got up, nightwolf had his green glow as he does in his shoulder charge and he hit throw and grabbed me and ya, he won

Maybe he pressed the throw button before you typed in the combination for Nightwolf's Shoulder Charge

Or another one is since you where at the end of the screen did you go past him or did you stay in front of him?

Maybe this was just a case of the most perfect (and lucky) timing in the world, ever. I would not stress about this. Even if we all knew a throw beats a shoulder charge, Smoke's teleport, Cage's slide kick, etc it's not like anyone would ever actually take the risk of trying it. You will pull it off 1/1000

Actually I can consistantly beat the shoulder charge with throws. Its easy you just have to catch Nwolf in his start up frame. Its a slim window and there are better options (uppercut comes to mind) but its doable. Usually happens for me when Im throwing a spam happy Nwolf player.

Propery timed throws can beat several moves, but as others have said, the timing is so strict and it's contingent on having a predictable opponent who always uses the same wake up option, those two variable make it ill advisable to even try it, at least in hopes of taking the match.