Thanks for the replies.
It is definitely not dirt, as this holster is either carried IWB, or left in a safe that has about 10 desiccant pacts with no indication of humidity. The only moisture this holster receives is on hot days when sweat may get to it when being carried.
The more I look at it, the more I'm thinking that this is mold. I'm not too sure I want this holster rubbing on me for the time being.
If I choose to clean it with either the vinegar, lysol, or lemon juice, what is the method behind cleaning the holster with these chemicals? Would any damage the leather if left on for too long? Should I soak the whole holster, or just dab a bit on the effected areas?
I'll also look into freezing it or leaving it in the sun for a while.
Here are some more pictures:
And some of the other, non-discolored side: