What methods do the pilgrims' portraits in the prologue use to clue us in to the fact that people are pretending to be something they're not?
I'm going to assume you're talking about the character descriptions in the prologue here. To best give an example of character appearance vs. inner character, I think you should look closely at the Nun/Prioress.
She was so charitable and piteous
That she would weep if she but saw a mouse
Caught in a trap, though it were dead or bled.(25)
She had some little dogs, too, that she fed
On roasted flesh, or milk and fine white bread
Chaucer often states traits of characters ironically. For example, describing the nun here are "charitable and piteous" is ironic because she feeds dogs meat, milk, and bread instead of giving her excess food to people in need, as one who is really charitable would be expected to do.
Her coral bracelet provides another subtle clue to her character.
Of coral small about her arm she’d bear
A string of beads, gauded all round with green;
And from there hung a brooch of golden sheen(40)
On which there was first written a crowned “A,”
And under, Amor Vincit Omnia.
The nun is often described as having one foot in the earthly world and one in the spiritual. During the middle ages, coral was considerd a defense against worldly temptation and a charm for love. Her bracelet and brooch with the words "love conquers all" subtly indicates her struggle with earthly temptation, though her manners are described as impeccable, and she strives to maintain the appearance of being a perfect nun.
Throughout the Canterbury Tales Chaucer provides hints such as these to indicate that the words he uses to tell about one's character may be ironic. Consider characters' appearances especially carefully when reading.