Fix $A, B \in \mathbf{\Delta}_{1}^{1}$ (i.e. they're Borel). Is the statement $A \subseteq B$ generally only $\mathbf{\Pi}^{1}_{1}$ (at best)? Of course, it's $\mathbf{\Pi}^{1}_{1}$ via $\forall x[x \in A \rightarrow x \in B]$.
EDIT: Here's my situation in more detail. For each continuous function $f\in C[0,1]$, let $S_f \subseteq [0,1]$ be a $\Sigma_{3}^{0}(f)$ set (that is, a set that is lightface sigma zero three in $f$) and for each $e\in \omega$, the set $Q_{e}\subset \mathbb{Q}$ is finite and computable (uniformly in $e$). I want to know the complexity of $\exists e[S_{f}\subseteq Q_{e}]$. In general, must I have a set (i.e. real number) quantifier to express that subset relation?
Even in the simple case where all of the $Q_e$ are empty, the complexity you asked about can be complete $\Pi^1_1$. To say $S_f\subseteq\varnothing$ is to say that $f$ is outside the projection of the binary relation $R(f,g)$ defined as $g\in S_f$. Even for quite low complexity relations $R$, the projection can be complete $\Sigma^1_1$, so the complement can be complete $\Pi^1_1$. Here "quite low complexity" depends on the space $g$ ranges over. If it were the Baire space $\omega^\omega$ then closed sets would be complex enough. For your situation, where the space is $[0,1]$, one needs to go a little higher in the Borel hierarchy, but I believe $\Pi^0_2$ (i.e., $G_\delta$) is enough.