The act of thrusting, which is the back-and-forth movement of the penis inside the vagina during intercourse, will typically tap on the cervix (the opening to the uterus). This is a normal part of the act and most women do not even feel it.
However, some women are more sensitive to cervical tapping and may experience ‘deep pain’ especially when in the missionary position. Common reasons for such sensitivity include being new to the act of intercourse, recently having given birth, or a uterus that sits lower in the vaginal canal.
A helpful tip: place a pillow under her buttocks so that her pelvis is higher than her waist, which will make the uterus slide back and give more ‘room’ for the thrusting.