7 weeks based on last period but gynae says embryo is showing 5 weeks

Hello all I need your views. The last 10 days I had very terrible appetite and very fatigue. The thought of what to eat next makes me nauseous and every smell is bad. Just this morning, I started feeling better (no longer extremely exhausted, my boobs are larger but no longer sore, and I am able to eat but still gagged out of the blue) Had my first gynae appointment in my life where my doctor told me there is only an yolk sac hence I’m at week 5 instead of 7 and prescribed me Duphaston. Is this a bad sign? I read Duphaston is to prevent miscarriages. Is my situation pessimistic? #firstbaby