Oxidation of the Nicotine in e-liquid will make it turn darker, as will the reaction of the various flavour ingredients, mostly it means your liquid could do with more steeping time, however another reason could be that you've had poor wicking or been running too hot and have burrnt the cotton slightly, the carbon will then discolour the liquid - easy way to tell is to turn your tank to a 45 degree angle and rotate it, if you get dark swirls at the bottom near the coil then it's coming from the coil otherwise it is just normal oxidation changes...