Last year I noticed that my female three-toed box turtle had a small hole in her shell. I thought that it might be from my male. While attempting to mate, he grips her around that area. I decided to watch it and see if it healed. It seemed to get smaller, and she went into hibernation. However, this year I noticed that she has another hole on the other side of her. I also noticed that my male's shell seems to be not growing in a certain place. These deformities are all between the same scutes. Because of this, I think that it may be due to some sort of nutritional deficiency. I'm not sure what it would be, though. I sprinkle vitamin powder and cod liver oil on their food 3-4 times a month. They live outside, so they get plenty of sun. Some sort of parasite, maybe?
Below are some pictures. The first one is my male's shell. The second is the hole in my female's shell that I noticed this year. The third is the one I noticed last year. Any ideas?

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