First of all, to make sense of "reduction mod $4$" you need to assume that $S$ is defined over $\Bbb Z$. Formally, the points of $S$ modulo $4$ are none other than $S(\Bbb Z / 4 \Bbb Z) = \mathrm{Hom}_{\mathrm{Spec} \, \Bbb Z}(\mathrm{Spec} \, \Bbb Z / 4 \Bbb Z, S)$, which would not make sense if $S$ was only defined over $\Bbb Q$. It does not make sense to talk about the integer points of a variety over $\Bbb Q$ a priori: the equations $x-3=0$ and $2x-3=0$ define isomorphic (zero-dimensional) varieties over $\Bbb Q$, but not over $\Bbb Z$ (the first one has a $\Bbb Z$-point, whereas the second one does not).
Assume $S$ is defined over $\Bbb Z$, then. Without further assumptions, it may very well happen that Hensel's lemma does not apply. Consider for instance the (zero-dimensional) variety defined over $\Bbb Z$ by $x^2-8$. There is exactly one solution modulo $4$, but there is none over $\Bbb Q_2$ (such an $x$ would need to have $2$-adic valuation $3/2$). What is missing is a smoothness assumption. You might have seen that for a single variable polynomial $f$, a solution $\alpha$ modulo $p$ is required to be a single root in order to lift to $\Bbb Z_p$; requiering $S$ to be smooth is the natural generalization of this condition to higher-dimensional varieties (technically we only need to assume that $S$ is smooth over $\Bbb Z[1/2]$ but I will ignore that).
Assume $S/\Bbb Z$ is smooth. Then indeed, any $\Bbb Z / 4 \Bbb Z$-point lifts to a $\Bbb Z_2$-point. But uniqueness only holds in the zero-dimensional case, and fails in general. For instance, take $S = \Bbb A^1$ the affine line over $\Bbb Z$, which is smooth. Then $S(\Bbb Z / 4 \Bbb Z) = \Bbb Z / 4 \Bbb Z$ has four points, each of which lifts to infinitely many points in $S(\Bbb Z_2) = \Bbb Z_2$. Hence as soon as you are working with positive-dimensional varieties, you may have a single point modulo $4$, and yet lots of them over $\Bbb Z_2$.
If you are working with a smooth, zero-dimensional scheme $S / \Bbb Z$ defined by monic polynomials, then having a single solution modulo $4$ does mean having a single solution over $\Bbb Z_2$, and these actually constitute all solutions over $\Bbb Q_2$! As $\Bbb Q$-points inject inside $\Bbb Q_2$-points, you have found that your variety is in fact made of a single point over $\Bbb Q$!