We had intercourse, he never pulled out, I didn't get my period in December, I am spotting

I got the birth control shot in October: and it only lasts 3 months. The whole time through December and January me and my boyfriend had unprotected sex. He never pulled out. I never got a period decemeber. And in the middle of january we had sex and I randomly started bleeding after that. It was spotting brown stuff and I hurt and cramped extremely bad. It went on for four days and then stopped. And a week later I started spotting once again. It's dark brown sometimes even looks black. It comes and goes. I have felt extremely tired and no sleep is enough. I get dizzy a lot. & the last 3 nights I have thrown up and I feel like i have acid reflex. Which I have never had in my life. I also pee a lot too. I took two pregnancy tests in December and one in January, they were both negative. Could I be pregnant? Even though it said negative( like could IT have been to early to tell?)Or is this side effects of the shot? Please help. Thanks in advanced!