I have noticed that some of the yeast, which are the normal tan color in the carboy, have become darker during their time in the bottle. Not sure what to attribute that to, but I haven't noticed any flavor issues from it. Are you bottling in clear bottles? If they are brown, it may just look darker than it is. Also, is it just the one bottle? If so, you might just take some extra care in the storage and handling of that one.
My guess though is that it is just some sediment from the brewing process that got through to the bottle (hops, grain, etc.). But the only thing you can do is wait it out now. If it were infected, you won't have any doubts when you go to take that first taste.
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Primary 1) Empty
Secondary 1a-f) - 2 gallons Traditional Mead, 4 Gallons Melomel, 2) Wee Heavy Widgeon Ale, 3) Pintail Pale Ale
Bottled - Amber Ale, TheJadedDog's All Amarillo IPA x2, Apfelwine, Wit Bier, Stout, Pintail Pale Ale (V1-Cascade, V2-Amarillo), Graff
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