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Because the cranberry sauce is brought to a boil and simmered for 10 minutes, it's likely that they will have split. That is okay!
As for the color of the finished vodka, there are a few possibilities: it may be from the darkness of the brown sugar used, or perhaps because of how long the cranberry sauce was boiled (caramelized sugar turns darker). Another possibility is that you didn't pour the full amount of vodka into the bottle after pouring in the cranberry sauce -- next time you might try mixing all of the cranberry sauce and all of the vodka in a bowl, then pouring from that into your bottles. Good luck!
You could also give it a bit of clarification with egg whites. Much like you would when making a consomme.