Empty sac 9 weeks according to lmp

I went for my ultrasound on Tuesday they found an empty just gestational sac according to my last menstrual period I'm supposed to be nine weeks and four days but according to the scan I was only six weeks and two days? I'm very confused by this so do I just add three weeks to my last menstrual period. That would put me getting pregnant around a week later than I thought I ovulated. ... The doc didn't give me much hope though. He said my chances are very slim of anything showing up :(