The phrase thalāthata qurūʾ combines two distinct issues. Thalāthata determinately means three, not two. What jurists discuss is which sort of periods qurūʾ denotes.
Number: three.
Units counted: menstrual periods or periods of purity.
Legal-method lesson: one part of a text may be unambiguous while another part raises a genuine lexical question. It would be mistaken to transfer uncertainty about the noun to the number itself.