One of the easiest ways to detect a rabbit or squirrel that may not be fit to eat is to check the liver when you clean the animal. The liver should be a nice consistent color and clean in appearance. If the liver has white, or sometimes yellowish, spots on it then there is a good chance that the animal has some sort of disease or internal parasite and you should probably not eat it. Other than that other indicators would be the general overall appearance of the squirrel. Plainly put,,, it should look healthy,,,,, fur clean and full, free of lesions and the animal should appear normal and healthy when observing it's ability to run, climb, etc.
It's very rare that you will run across a squirrel that is unfit to eat. Mother nature is very efficient when it comes to eliminating, or culling, sick or diseased animals. They usually don't last long or are easily killed and taken by predators.
Hope this helps ya.
Jeff