All PCIe graphics cards have 2 short pins as far as I recall. Maybe more. These are actually short by design.
Click on the picture on this link, and look at the front and back side of the card. You'll notice that there is a short pin on both sides of the card.http://www.newegg.com/Product/Product.aspx?Item=N82E16814130656
If that is what you noticed on your card, then don't worry, that is by design.