What you wrote is not exactly right. The function $f(x,y)=\frac{x^2-y^2}{(x^2+y^2)^2}$ is not integrable with respect to the Lebesgue measure on the unit square $(0,1)\times(0,1)$ (so it does not fulfill the hypothesis of Fubini's theorem), but the integral
$$ I=\int_{0}^{1}\int_{0}^{1}\frac{x^2-y^2}{(x^2+y^2)^2}\,dy\,dx$$
does exist, since:
$$ \int_{0}^{1}\frac{x^2-y^2}{(x^2+y^2)^2}\,dy = \frac{1}{1+x^2} $$
hence:
$$ I = \int_{0}^{1}\frac{dx}{1+x^2}=\arctan(1)=\frac{\pi}{4}.$$
However, it is straightforward to check that:
$$ \frac{\pi}{4}=\int_{0}^{1}\int_{0}^{1}\frac{x^2-y^2}{(x^2+y^2)^2}\,dy\,dx\neq \int_{0}^{1}\int_{0}^{1}\frac{x^2-y^2}{(x^2+y^2)^2}\,dx\,dy = -\frac{\pi}{4}. $$
The integral that is not defined is:
$$ \iint_{(0,1)^2} f(x,y) \,d\mu $$
where $\mu$ is the Lebesgue measure on the unit square.