has suggested, that is a normal thing. Water quality and health may also influence the vibrancy of their coloration. If your fish's colors seem a little dull, over a couple of days make a couple of partial (40%-50%) water changes, with properly treated water which has sat open for a day or two and is the same temperature as the tank. See if the discoloration fades.
If there is a way of knowing if the guppies were raised in a pond for a time, there is also a fairly benign "black spot disease" which wild and pond raised fish may carry. Especially common among cichlids collected in the Great Lakes of East Africa, they are a fluke which can cause part of the skin to turn into dark blotches. That can also look like someone smeared a little felt tip marker on the side of the fish. It can not be passed on to other fish unless you have fish eating birds flying around your home. ;)
Burgess Bailey and Excell's book suggests there is a remote chance that some wild snails may also carry it. They say that there is no cure. But http://watershed3.tripod.com/diseases.html
suggests that salt baths may help.
Here are a couple of examples:
http://ag.ansc.purdue.edu/courses/aq448/images/blackgrubgross.jpg
http://www.fishdeals.com/fish_diseases/black_spot/black_spot.gif
http://eekers.paper-tigers.org/pond/symptommm.jpg
This has nothing to do with your fish, but your question made me think of it. At fish shows we've been known to kid one another about fish becoming suddenly absolutely stunning in color. In one case I leaned over to the owner and, in a stage whisper, suggested, "Yeah, those are death colors!" ;)
All the best!
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