Johnny, often what happens is that if you're thrusting fairly deeply and perhaps slightly at an angle, you can bump into the area where her ovaries are inside, and that's a very tender internal spot and can cause significant pain. The parts of the female reproductive system are all quite close together up in there, which means a deep thrust can sometimes inadvertently poke a tender area. This tends to happen more when you're in the standard guy-on-top missionary position.

When she's on top and is able to control the depth of the thrusts a little better, you won't be as likely to run the risk of thrusting into the area where the ovaries are. Work on slowing down and taking shorter, slower, shallower strokes or let her take the upper position, and you'll avoid that problem in the future. Good luck!