I also see a sore possibly on the top of her beak. Could she have injured herself on a sharp feeder or some metal fencing? Could you show a picture of the front of her beak. Fowl pox is very common this time of year, and it can cause scabs in colors from light tan to dark brown.
The bump on her beak looks similar to other bumps on other chickens that have been posted over the years here on BYC. Sometimes they have been thought to be caused by a papillovirus, and some have said that they eventually fall off. Some think they can be the result of a cut on a sharp feeder or piece of fence.