Does endometriosis cause pain during penis penetration?

Absolutely: The inflammation in the pelvis due to endometriosis is often located deep in the pelvis just behind the uterus and cervix which means it is just above the top of the vagina. This area is indeed, during penetration apt to get bumped and can indeed cause what is called "deep dyspareunia" (pain with deep penetration). A very common cause of this pain is endometriosis.