If you can, pictures will help you get the best response.
Generic response: Colonies of lots of different critter types will pop up on your live rock as time goes on. Your rock will eventually have splotches of many different colors. It's not necessarily a bad thing.
One dark spot I often see in my tank is an algea called lobophora. It starts out a dark circles and grows as a mat over the live rock. It can be tan to black. If it grows to excess, it can overgrow corals and other things clinging to the rocks. Control of this algea is the same as all algea: nutrient control.
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