Hi 1981,
You could be correct in your assumption of him pushing 'things' around down there. Because you have the cysts that the sperm have to get through which is why conception actually takes awhile when you have the cysts. I have heard that pregnancy helps with cysts and makes you more likely to conceive again. If you feel any pain get to the ER or the doctor immediately because it might mean that you have an ectopic pregnancy which is very painful for you and fatal for baby.
Now, I'm not sure if he is bf or husband, but for his sake you will have to get a DNA test. Just because you had sex using protection doesn't mean nothing happened to the condom that you used with him, maybe it had a small hole in it, who knows. I know it's hard on couples when you are TTC and are not, a lot of people get accusatory on the other, who knows what it actually was but I am hoping that it is your husbands.
Is it a problem for you that your bf or husband is not hung? Are you constantly thinking of your friend who is hung? If so, you might need reevaluate your relationship before the baby is born, parents constantly arguing and fighting is very hard on children and frankly, not fair.
Good luck and hope this helps