I would be willing to bet what you are seeing on the squirrel liver are canine tapeworm cysts. They are very common in squirrels and rabbits. They usually pick them up from fleas that fed as larvae on dog or other feces that contained the tapeworm eggs. When the squirrel or rabbit groom themselves they eat the cysts in the eggs and then the eggs hatch into cysts and hang around in the entrails of the rodents. In my area of PA we call them beads, the real old timers used to say don't hunts rabbits or squirrels until the first killing frost and the beads will be gone. That is lot of rubbish since the beads are in the insides. They are very easy to see on the liver because of the color, they look kinda like a tiny egg, a clear sunstance with a white yolk. I suspect if you go through the entrails you will find them there, they're just harder to see. There is nothing wrong with the meat from animals that have these cysts, they are only on the entrails and not in the meat. I have eaten hundreds of rabbits with them and some squirrels as well. When you see raised white spots that look kinda like cottage cheese, that is when to bury the carcass so no dog eats it because that is a sign of tularemia, rabbit fever. Sadly a lot of rabbit and squirrel meat is wasted because hunters don't know what those tiny white cysts are. Picture below of a real bad infestation in a rabbit.
