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You are referring to the black velvety patches on the sand and glass right? If so, that is called cyano bacteria. It's a result of excessive nutrients present in the tank. You can simply siphon it off or gently brush on it to take it off while doing PWC. Just be careful not to siphon the sea ponies also, it may help if you reduce the feeding to very small amount and spread it over a more frequent intervals. That way you can make sure the ponies eats most of the food with little left overs. Also, you might consider cutting back on the lighting since they are photosynthetic. Good luck!
Ok, figured out the issue! So the dark patches on the sea horses are from stress. It could of come from the cyano. Basically, anytime everything is not absolutely perfect they freak out like that.