Not Just Yellow
Yellow fungus is a deadly fungus that is highly contagious among bearded dragons. This fungus is slow growing but eventually will kill a bearded dragon. There are treatments for this fungus, but there is no cure. The fungus is not always yellow as the name suggest it can also be varies shades of brown, tan & black. It slowly destroys a dragons skin and causes a dragon to become inactive and stop eating. If your dragon had odd shaped patches that are off color, seek a reptile vet's opinion as soon as possible, but please don't confuse discolored skin with shedding skin. If your dragon has a discolored patch of scales that has been different for over a month seek out a reptile vet immediately.
Photos from http://www.beautifuldragons.com/yellowfungus.html and google images