Found out I was pregnant today but it came with a twist

So I went to the gynecologist today for a discharge problem,that lasted a week after my period had already ended on Dec.7th and she said it was just one of those periods that just went wonky and it was normal for that to happen but what really got me is when she ordered a pregnancy test and it came back POSITIVE. I was and still am in shock but the crazy thing is the gestational sack the baby should be in is in my uterus(saw the ultrasound as she was looking and she pointed it out) but the baby isn't so I have to go back Saturday to see how my levels are to see if it's a viable pregnancy(doctor thinks it was too early into my pregnancy to see anything on the ultrasound today) or if I had a miscarriage this whole time without realizing it and thinking it was a period instead.

Update: December 23,2016

So I went to the doctor this past Tuesday and the ultrasound showed I had an ectopic pregnancy with some free fluid surrounding a cyst on my right ovary. Thursday I went in again and the free fluid had increased in volume and the cyst seemed to have ruptured so I had to have surgery to remove it and stop the bleeding. I'm currently at home resting.