It could be the wet form of fowl pox if there was still some pox floating around the coop with shed scabs. But canker also can cause yellow plaques inside the beak and throat and down into the esophagus and crop. Does it smell bad? Canker tends to have a bad odor, and is brought in by wild birds and pigeons. Canker is treated with anti-protozoan drugs, such as Fish Zole (metronidazole, Flagyl) and ronidazole, which can be found on fish and pigeon sites. There is no cure for wet fowl pox, as it lasts several weeks.