They say you can't judge a book by its cover, but in the many worlds of A Wrinkle in Time, the book may be in an entirely different universe from its cover. The book-cover analogy is surprisingly apt – how can an artist ever capture the complexity of most books in a single image? A Wrinkle in Time suggests that our experience of the world is similar: we see flashes of something larger, but the thing itself always extends beyond our reach. Appearances may be deceiving, but at the same time they're all we have to work with.
While the initial appearances of Mrs. Whatsit and the Prime Coordinator appear to be deceiving, the specific language used to describe how they look gives strong clues as to their true natures, suggesting that appearance is not so deceptive after all.
The transformation of Charles Wallace suggests that the effect of a person's appearance is inextricably linked to what's inside them, so appearances are never entirely deceiving.