In general, there is no problem covering a pot of fully cooked food on Shabbat. Since it is already cooked, the covering does not enhance or speed up any cooking. However, Rav Shlomo Zalman Auerbach (Jerusalem, 1910-1995) held that it is prohibited to cover a pot containing chicken bones, even if the rest of the food is fully cooked. The bones give the pot a different status, because if cooked long enough, the bones will become edible. Therefore, even if the rest of the food is fully cooked, the covering will accelerate the cooking of the bones.
Hacham Ovadia and Rav Moshe Feinstein (Russia – New York, 1895-1986) held that if a person does not normally eat bones, there is no problem if the bones become cooked. Even if he does eat marrow, it is not a problem, as the marrow is most probably cooked with the rest of the food. But, if he does eat bones, he may not place a cover on the pot.
If one is accustomed to eating chicken bones, he may not place a cover on a pot of otherwise fully cooked food that contains chicken bones.