Hi Anna. First, I'd just like to welcome you to the forum, so welcome.
Most eliquid will darken with age. It's the nicotine reacting with other ingredients in the mix (usually stuff in the flavoring concentrate). Air and light will speed this process up. It doesn't hurt anything.
That said, what you're probably experiencing here is backwash. Residue and deposits that have formed on the coil are finding their way back into the cart. This is fairly common and doesn't really hurt anything as far as I know, other than maybe affecting the flavor a bit. It's not caused by anything you're doing or not doing, so you're not doing anything wrong. I've never bothered cleaning an atty. There are many methods to do this if you want to try, but since I don't do, I'll leave that subject for someone else to talk about. Like you, I just give my Tank attys a blow through if the draw is getting too tight (you have to suck harder to get a hit). I do rinse out my Tank carts between fills with hot tap water. But if the flavor starts getting bad or the atty performance starts dropping off to the point where you're not getting a satisfying vape, you should either clean them or just start using a new one. And that's something you should be aware of... most attys don't just "die", but rather the performance will drop off slowly over time. Often, you may not realize how much the performance has diminished until you break out a new atty. Occasional atty cleaning or replacement is necessary to keep you happily vaping along. Just how long an atty will last (yield a satisfying vape) depends on how much of a performance hit you're willing to live with and how much you vape. Unfortunately, the consistency of attys varies widely too, so some will outperform and outlast others. Hope this helps set your mind at ease a bit.