Why does my dog wake up coughing and breathing heavily at night?

I am sorry to hear about your dog. This lesion could be an insect bite, an area of bacterial or fungal infection, or growth. Without seeing it in person it is difficult to distinguish between these. The coughing is much more concerning and I would recommend having her examined as soon as possible if she is having ongoing coughing and difficulty breathing. Some conditions, such as heart disease, can cause coughing that is worse at night when the pet is laying down, so I would want to examine her, listen to her heart and lungs, and take an x-ray of her chest to determine just why she is coughing. Heart disease is not common in a 9 month old dog, but we would also want to check for things like congenital diaphragmatic hernias which could cause problems when she is laying down, or infections of the respiratory tract.