Discolouration when boiling green vegetables with lid on
See mines's link. Also, leaving the cover on a pot of boiling water increases the pressure inside the pot, which raises the boiling point, which in turn increases the temperature of the water (as it can no longer bleed of excess heat through steam). This principle is used by pressure cookers to get the water really hot to quickly cook the contents.

Basically, you're overcooking the vegetables.