Recall the manner in which Milnor defines the differential of a map $f: X \to Y$ at a point $p$. To Milnor, all manifolds are embedded as subsets of some Euclidean space $\Bbb R^n$; we pick a smooth extension of $f$ to an open neighborhood of $X$. For us it will suffice to pick $f(x,y,z) = (x,y)$, where $f$ is now defined on the whole of $\Bbb R^3$. You should verify, using Milnor's definition, that the tangent space at a point $p \in S^2$ is precisely $T_pS^2 = \{h \in \Bbb R^3 | h \cdot p = 0\}.$ Now, if $h \in T_pS^2$, write for convenience $h = (h_x,h_y,h_z)$. By definition, $$df_p(h) = \lim_{t \to 0} \frac{f(p+th)-f(p)}{h} = \lim_{t \to 0}\frac{(th_x,th_y)}{h} = (h_x,h_y).$$ Because the codomain of $df_p$ is, as you mentioned, 2-dimensional, to find where $df_p$ is not surjective you need precisely to find what $p$ it's not injective for.
But $df_p(h_x,h_y,h_z) = 0$ iff $(h_x,h_y) = 0$; and the vectors $p$ such that $(0,0,1) \in T_pS^2$ are precisely those of the form $(x,y,0) \subset S^2$. These are the points in $S^2$ for which $f$ is not regular.
The intuition you should have for what's going on here is that in this situation, where we have a map between manifolds of the same dimension, that map $f$ has $p$ as a regular point precisely when $f$ is a diffeomorphism when restricted to a sufficiently small neighborhood of $p$. For points in the upper and lower hemispheres, this is true; but $f$ is not even injective on any neighborhood of a points on the equator.