Once in a while, not very often, I have a small amount of ejaculate come out while im on the toilet... my wife and I are also going through infertility treatment...  (beginning stages) could there be a connection between not getting pregnant yet and the semen coming out while pooping?
Semen coming out while pooping is not that abnormal, that too if it is once in a while. I would advise you to confirm that it is only semen and not pus due to infection. Just submit the discharge to the laboratory to confirm what it is. If it is pus or any discharge indicating infection, it will definitely hamper the fertility. In that case you will have to undergo an antibiotics' treatment. Anyway, both of you are undergoing infertility treatment. So all physical and laboratory investigations must be on the card. In that you may suggest the physician to find out whether you have got any urinary or genital infection. If there is no infection, do not worry about semen coming out while popping. There is no connection otherwise with infertility.