What you're seeing is simply the surface of the good metal that was under that rust before you removed it. EvapoRust is not supposed to attack the metal, and I've let things, including planes, soak MUCH longer than you did with no damage. All EvapoRust does is remove the rust; it doesn't turn the rust back into elemental metal. It also leaves a residue that has to be cleaned off by methods that others have already explained. But you didn't do anything to cause the damage to the surface of the metal itself. The corrosion process caused it before you ever got the plane.
There is, however, one strange effect of EvapoRust that I've noticed and can't quite explain. After I've used it to clean chisels and other edge tools that have carbon steel inlays, the inlay is sometimes quite a bit darker than the other metal. But even then, the chemicals don't seem to cause any surface damage.