Apparently (and I'm not saying this is the case here, but it could be) a woman's ovaries are as sensitive as a man's testicles, but obviously being internal they don't get hit so very often. It has been recorded previously that some women when they have sex do experience pain here if the penis forces some indirect contact with them.
If it's only pain when in one position, I doubt there's anything seriously wrong. Try moving position slightly and see if that helps, or going gentler. More than that, I can't suggest really.