Let the square $S$ be the set of points $(x,y) \in [0,1]^2$
Let $R \subset S = S \cap \mathbb{Q}^2$, that is, the "rational pairs" in the square.
To each of these points $r_i \in $ R, we can associate a small square $s_i$ of area $\epsilon / 2^i$, centered at $r_i$. Now the collection $\{s_i\}$ must cover $S$ because if any region of $S$ is uncovered, then that region contains a rational pair that is uncovered which is a contradiction.
So since we covered $S$ with a buch of small squares $s_i$, then $\text{area}(S) \le \sum \text{area}(s_i) = \epsilon$
Since $\epsilon$ was arbitrary, the area of a square is $0$!
So what went wrong here?