Shapeshifters do not have the same rods and cones in their eyes that we do. We as humans see a limited selection of color, from just above infrared to just below ultraviolet, through a filter of red, green, and blue light. Shapeshifters, however, can see beyond that, into ultraviolet and infrared, and in far greater scope than just three colors. Their abilities aren't perfect; while they may look like a human to a human, to another shapeshifter they are covered in stripes, swirls, dots, and blotches of color.
Just like a black-and-white picture hides the colors of the actual scene, our eyes hide the colors we can't perceive - and the shapeshifters use those specific colors to tell each other apart: Alice has a gred squiggle on her arms, Bob has blurple stripes on his face, and Claire's legs are entirely bleen - though to human eyes, Alice looks ordinary-human-pale, Bob looks ordinary-human-tanned, and Claire seems to be ordinary-human-dark-skinned.
Certain creatures, notably the mantis shrimp, can see the shapeshifters' true colors, but can't (or won't) mention the visual difference.
Additionally, as Mark Storer mentioned in his comment, the shapeshifters may have (replacing or in addition to extra light sense) polarized skin tones. While sunglasses would pick up linear polarization, they wouldn't detect circular polarization - though 3D movie glasses would. Linear polarization may be picked up by reflection, too, so it makes sense for the shapeshifters to have circular polarization. The polarization filters would likely be a key part of the creatures' ability to shapeshift, as it would control color and brightness.