If you assume that different substances are radiating at different wavelengths, the obvious conclusion is that some of these substances are moving faster (or slower) than the rotation of the star: in other words, winds. Think of the stripes on Jupiter. Or perhaps these are different layers within the atmosphere:
These variations are the result of different layers or patches of material swirling around the brown dwarf in windy storms as large as Earth itself. Spitzer and Hubble see different atmospheric layers because certain infrared wavelengths are blocked by vapors of water and methane high up, while other infrared wavelengths emerge from much deeper layers.
"Unlike the water clouds of Earth or the ammonia clouds of Jupiter, clouds on brown dwarfs are composed of hot grains of sand, liquid drops of iron, and other exotic compounds," said Mark Marley, research scientist at NASA’s Ames Research Center in Moffett Field, California, and co-author of the paper. "So this large atmospheric disturbance found by Spitzer and Hubble gives a new meaning to the concept of extreme weather."