I Am In My Second Year Of The Second Generation

I am in my second year of the second generation Implanon. I am having abdomen pains, tender nipples, little weight gain, very high appetite and 6 days late on my period. My implanon is broken, doctor at emergency room has confirmed. My boyfriend and I have unprotected sex almost daily. Tests are negative. Can I get false negatives? Will it hurt the baby if I am and still have the implanon in?