Dear Darshan, Apologies for I missed your question to answer.
Do you mention that nostrils got black from inside? If so, did you use baking soda or alum water? Their use causes such reactions. And only salt is required to be used in neti water and blacking of nose because of neti with salt luke warm water has not come across earlier. Please elaborate how do you do neti so that we can analyse the situation and then suggest accordingly.