Stomach pains and sickness, but test was negative

I have been on the pill for some time now, but my doctor changed it to where i am taking them non stop so i wont every have period but every 3 months sweet right. Not really me and my boyfriend have had sex with out a condom and he has been cuming in me. I missed my pills for 2 days straight after the last time we had sex. I would say about 2 Saturdays ago. Not for sure though. I had missed my pills the after and it was the week i was pose to have my period but of course i didnt because i took the 2 pills i missed on monday. I had been experiencing bad pains in my stomach in more then one area at different times, throwing up, but i have also been sick from my allergies. so i had mucus in my throat too. But i went to the ER for the pain they did a test and it was negative the took a cat scan and said i need to just poop more. I dont think its in my head this time. Is there any way the sperm could have stayed in for those two days and caught an egg. Im only 16 and i need help.