Tanafur al-huruf concerns disharmony among the sounds within a single word; tanafur al-kalimat arises from an awkward succession of otherwise meaningful words. These defects are not simply violations of morphology or syntax: the cultivated auditory judgment of competent speakers plays a role.
The source refers to المستشزر and to harshness arising between neighboring words. A word may be individually acceptable yet difficult in a particular sequence.
It is therefore insufficient to verify that every word occurs in the lexicon. Their combined sound and articulation can also affect fasaha.