Hi, thanks for asking! I'll tell you everything about my very, very basic "method" but I have to admit that I am not an expert myself and have not learnt this method from a leather specialist either. So, even though it worked for my bag particularly, I would still advise you to ask people who are more knowledgeable and can provide much more refined and reliable ways of removing stains.
I usually wear my Niki as a shoulder bag with double chain, not as a crossbody, so even though I wear denim jeans pretty often, the leather was not touching denim and was not getting stains therefore. Once I wore it as a crossbody while I was wearing dark blue jeans, and after couple of hours I noticed very thin but visible stains on the back of my Niki. At first, I decided that I would bring it to Saint Laurent boutique immediately and ask for repair service. Then I realized that as long as Niki's leather is crinkled and not smooth, I could probably clean the stains myself. I would never risk it if it was smooth or more delicate leather. So, I made my fingertips wet with just a drop of water and as simple and ridiculous it may sound, I cleaned the stains directly with my fingers and nails. The linings of the bag are more gentle and harder to clean, so, I did not use my nails in that case to avoid scratches and used only fingertips (the same applies to the leather part of the strap as well). The leather looks perfect without any trace of colour transfer (original colour has not faded either), however I understand that it is very unprofessional way to take care of leather, so I would probably not recommend to repeat it, especially if you like to "baby" your handbags. Also, I tried this just three times even though it's been almost a year since I've bought the bag, but I understand that using this method often may damage the leather.
I guess my experience is not very helpful, but at least it demonstrates that Niki is a very practical and durable bag that can be worn often and still look pristine. Anyway, if you are afraid of colour transfer, just try to avoid dark denim while wearing the bag. I hope you'll enjoy wearing your Niki!