Help?

I took a pregnancy test this morning & got a really faint line.. Went to the dr. Today & had a blood pregnancy test done & they said I was pregnant but my levels were at 12 & I would be 4 weeks & 5 or 6 days. He said that's not what he would like to see around this time. My question is could someone help me understand this better & help me learn what I should expect. Will my baby be okay?