A basic mixture of MHRB was kept in a cool dark place for about a month. Naphtha was recently added to this mix a few days ago, and at that time, the volume has somehow decreased. The jar was shaken many times and was ready for pulling. Now, however, it appears as if there are crystals already sticking in between the NPS and the basic soup. There are even some chunky crystals appearing on the sides of the jar and small ones floating in the solvent along with what appears to be tree fats and oils.

I have never seen this before and the only post I could find was one regarding foam. The solvent is too murky brown to do a pull and there is a lot of white on the surface of the basic mixture. Why is this happening and what should one do in this situation?

I have seen this too.

If it is spice you could try to redissolve it by warming. Another option is to try getting it out by pouring through a metal tea strainer or fine sieve or similar (I used a tea strainer, I think the smaller size is probably easier).

If you get it out by pouring through a sieve it will be dirty. I cleaned it by initially putting into a glass of cold water then decanting, this can be followed up by a re-x or 2.