It happens if you dilute it in DI water solution. If you keep the same percentage of organic solvent, it should not happen. Either organic solvent like MeOH or alkaline solution (basic water) can increase its solubility.
We usually dilute quercetin with water for cell culturing with RPMI-1640 solutions. Quercetin in a water solution, depend on concentration, could induce a distinct effect on cell proliferation or apotosis induction. I think that quercetin concentration or some not polar organic ingredient could be a reason of quercetin precipitation. Maybe something included in this assay. The good idea is to ask assay producer for advice.