Upon further examination, it seems to me that your coil has a bit of buildup on it, and when you drip liquid on it, some of that buildup flakes off and ends up on the cotton. To confirm the presence of buildup, pull the atty apart and look under the bell housing, or under the top cap. Buildup comes from certain juices that are either NET (Naturally extracted tobaccos) or have a high sweetener content in them. Usually the latter of the two. If it's too bad, your vape will start having a burnt or "off taste" to it. Can be remedied by pulling the wick, completely burning off all the "gunk" or "buildup", and rewicking. Try a different juice if the problem persists.
As for the organic cotton - it will have dark spots in it naturally. Could be parts of the cotton hull, seeds, etc. To switch to Rayon though... is to allow greater freedom in wicking. I love me some cellucotton! Best...wick...ever...hands down. Juice to juice switching without rewicking, cleanest flavors to date, and a lot more friendly when buying in bulk. Get a HUGE box of it for like... 25-30 bucks. A box lasts awhile too.
CelluCotton Beauty Coil 3lbs. - $17 for 3lbs of the stuff. I bought a 5lb box once.