I didn't see anyone mention the angle of penetration. For myself, sometimes a bad angle rubs the opening of the urethra, and that hurts. When this happened, I explained to my H what was going on, and changed his angle of entrance. Once he understood what angle was bad for me, he was able to avoid it.
Also, there was a time in the past when I had some deep abdominal pain during deep penetration. Sometimes it's a sensitive ovary (like during ovulation). Also I once had an ovarian cyst. It was benign, but it caused pain.
