This seems to be a basic misunderstanding. Although the paper is actually quite clear on this. Let's recall some basics:
A language $\mathcal{L} \subseteq \{0,1\}^*$ is a set of "words" or, in the context of proof systems more commonly, "statements" $x$.
An NP language $\mathcal{L}$ is generally defined by an efficient relation $\mathcal{R}$, such that $$\mathcal{L} = \{x\in\{0,1\}^*\mid \exists\; w\ldotp\; (x,w)\in\mathcal{R} \}$$
where $w$ is referred to as a "witness" of $x$.
What Groth16 would like to be, is a proof system for the language of satisfiable arithmetic circuits, which happens to be equivalent to a proof system for the language of satisfiable quadratic arithmetic programs.
In this setting, a statement $x$ would be a quadratic arithmetic program and a witness $w$ would be a satisfying assignment for that program.
Unfortunately it doesn't actually manage to do that, because it doesn't have a universal setup. So what does Groth16 actually do?
In Groth16 the Setup is for a specific quadratic arithmetic program, that defines the relation $\mathcal{R}$, statements $x$ are the publicly known inputs to this program and witnesses $w$ are the secret inputs to that program.
That is, purported statements are of the form $x = (a_1,\dots,a_\ell) \in \mathbb{F}^\ell$ and witnesses are of the form $w = (a_{\ell+1},\dots,a_m) \in \mathbb{F}^{m-\ell}$ and the specific NP relation for which Groth 16 proves something is defined by a bunch of polynomials $t(X)$ and $u_i(X), v_i(X), w_i(X)$ for $0\leq i \leq m$ as
$$\mathcal{R} := \{((a_1,\dots,a_\ell),(a_{\ell+1},\dots,a_m)) \in \mathbb{F}^\ell \times \mathbb{F}^{m-\ell} \mid \sum_{i=0}^m a_iu_i(X)\cdot\sum_{i=0}^m a_iv_i(X) = \sum_{i=0}^m a_iw_i(X)\} +h(X)t(X)\}$$
where for convenience of notation $a_0 =1$ and $h(X)$ is an arbitrary degree $n − 2$ quotient polynomial.
What all of this means, is that what the Setup algorithms receives as input, is not the witness and not even the statement, but a description of the NP-relation we're trying to generate proofs for. The NP relation is of course public anyway and therefore, nothing is being "leaked" here.