There is no disagreement between
A: John's eyes are black.
B: John's pupils are black.
Neither is there any contradiction between
C: John's students are black
B: John's pupils are black.
But in the sequence, A: B: C: the phrase
B: John's pupils are black.
changes its meaning, an example of total lexical ambiguity, in this case created by two words,
1 the homonym "pupils," schoolchildren (from puer +diminutive suffix) and "pupils" the centre of the eyes by metonymy fom the previous meaning here used for eyes by synecdoche,
2, the polysemous word "black".
The Cause of the Ambiguity is recategorisation or recontextualisation of phrase B:. The listener has made a category error.
This Process of Misunderstanding comes under the heading of pragmatics.
The Circumstance leading to the misunderstanding is universal lexical ambiguity.