There are two ways to dye thread. In one you dye the raw fiber before you spin the thread. This creates threads where the color goes straight through to the core of the thread. The other way is to spin the thread and then dye it.
If you use this method it’s possible for two things to happen. One is that the dye wears off. The second is that white spots show up if the twist is disturbed. If either of these occur it can look like a flaw in your needlepoint.
Pearl cotton is a thread that’s dyed after spinning and one that is prone to these problems. Needle Nicely has a great post explaining how this happens and giving a great tip for avoiding it. I’m trying it tonight!