6 week ultra sound showed heart beat in one sac and yolk in the other. Is this normal for naturally conceived twins?

Septate uterus? Was there really a second sac, or was it the same sac wrapped around a uterine septum? It is not impossible to have dichorionic twins missed before 6 weeks, but one has to consider all possibilities. Another scenario: vanishing twin syndrome or large subchorionic hematoma. Serial ultrasounds by an expert diagnostician will be required to tell the final diagnosis. Take Folic Acid 1-5 mg daily!
Not Really. Twin gestational sacs are more common than people think, but at 6 weeks you should be able to see normal embryos in both sacs if it's a normal twin pregnancy. You might have a viable (normal) single embryo & an empty sac (blighted ovum or anembryonic gestation). This will be followed & usually you end up with a normal single healthy baby. A f/u ultrasound should be repeated, good luck.