I am not very good with hatching problems, but chicks with unabsorbed yolk sacs may be weak and have poor immunity to infection because of the yolk not being absorbed. Leave it alone and isolated in the incubator to let the yolk sac dry up. I would give it some Poultry Cell vitamins or NutriDrench. Leg issues can be common with incubation. Here is some reading about yolk sacs: http://www.poultrydvm.com/condition/chick-yolk-sac-infection-omphalitis
A few pictures of the chick, navel, and leg area would be good.
I agree with Eggcessive. Chicks that have yolk exposed to the environment, need to be set in a sterile area to prevent the risk of infection. Since the yolk is prime bacteria growing material and is actually used often as an addition to agar for culturing bacteria, if any little bacteria gets on the leftover yolk it can spread rapidly, and sadly with most cases of yolk sac infection, the chicks often die.
Wearing sterile gloves, I would get a small cup, or bowl, line it with some dry paper towels, and set her in there for now, inside the incubator. Leave her be to absorb the rest of the yolk, then I would consider giving her a few drops of a poultry vitamin, or sugar water. After the yolk has shrunk up a bit, it might be good to dab some iodine, or an antibacterial ointment just onto the yolk area to help prevent infection.