You can color fast (http://requiemart.com/blog/tutorials/repair-tutorials/color-fasting/) clothing to help prevent stains :3 If you're really worried you could even get one of those things that attract excess dyes when you wash something. Red often has too much dye but very dark shades are generally known to be possible stainers, too.
Part of it depends on the doll (for example, vinyl will stain easier than resin) but there's probably many factors that go into it. Doll type, doll quality, doll color, fabric type, fabric quality, dye color, dye quality, weather (possibly?), how the doll/clothing is stored, how tight the clothing is, how often the doll's outfit is changed, etc. If I'm going to leave my softer or more sentimental dolls in the same outfit for long periods of time I try to pick something light in color and at least a little loose. Some people suggest storing dolls naked if you can but I'm generally not a fan of that.