My guess is that you're talking about squirrel pox, also called squirrel fibroma, which is a viral disease affecting gray and fox squirrels in many areas. It causes tumors and, in severe cases, organ failure, blindness, and death. Most infected squirrels probably recover from it, and it seems to have no impact on overall population levels. There is no known prevention or treatment, and it cannot be transmitted to humans. You probably notice it at this time of year because it affects mostly juveniles and because squirrel population levels are at their highest now.