What could produce dark green chunks after rinsing with scope mouthwash?

Food debris: This is an interesting one. It is probably just some food debris that got stained green by the scope. It could also be exudate from inflamed tonsils. Have you had a sore throat or other symptoms? On a different note, i would recommend listerine rather than scope. Scope is not really "medicinal" and is just a cover-up for bad breath.