When Jerry is trying to teach Mason math, Mason is suddenly able to solve complex equations with ease. But, he seems confused about the numbers themselves, saying "I can hardly see the numbers."
What Jerry means is that Mason is so focused on the "big picture" and the beauty of the math that he's losing sight of the individual numbers themselves. It's a funny way of saying that Mason's brilliance has become so overwhelming that even the basic building blocks of the subject seem insignificant in comparison.
This highlights the irony of the "Muse" spell: while it makes Mason brilliant, it also removes the joy of discovery and the struggle of learning that comes with mastering a subject.