This is due to pi stacking interaction between molecules quercetin.
Between the molecules of quercetin occur aromatic interaction (or π-π interaction). π-π interactions are caused by intermolecular overlapping p-orbitals in the π-conjugated systems, so that they become stronger as the number of π-electrons increases.
In other words, the polar substituents of one molecule of quercetin hang over the aromatic ring of the neighboring molecule. As a result of this interaction quercetin molecule hydroxyl groups are not capable of dissociating. This causes that quercetin is not soluble in water.