I think if he really is pregnant (which is very likely) he got pregnant from the very first time they had sex and he snuck into his bed. He came inside him, and then said "Sorry im not giving you anymore" and then put on a condom. That makes more sense with the timeline as well.
Next chapter and his reaction will be very important in regards of how this relationship will progress
I cant believe i read this comment like those people watching a match in a sports anime HAHAHAHA