Let $\mathbb{E}$ be the set of prime powers (except $1$). Let $f \in \mathbb{Q}[x]$ be a rational polynomial with $f(\mathbb{E}) \subseteq \mathbb{Z}$. Does it follow that $f$ is numerical, i.e. satisfies $f(\mathbb{Z}) \subseteq \mathbb{Z}$?
Notice that the set $\mathbb{P}$ of prime numbers is not enough, as the example $(x^3+x+2)/4$ shows.
Example. If $q$ is a prime power, then $(q^{10}-q^{5}-q^2+q)/10$ is the number of monic irreducible polynomials over $\mathbb{F}_q$ of degree $10$. Can we conclude from this directly that $(q^{10}-q^{5}-q^2+q)/10$ is an integer, for every integer $q$ (which I also know to be true for other reasons)?
No.
The polynomial $p(x)=\frac{x(x-1)(x-2)(x-3)(x-4)(x-5)(x-7)}{4}$ takes integer values with $p(x) \equiv 0 \bmod 8$ for all $x \not\equiv 6 \bmod 8$, but $p(6) \equiv 4 \bmod 8$. If $x$ is a prime power, then $x \not\equiv 6 \bmod 8$. It follows that $\frac{p(x)}{8}$ takes integer values at all prime powers, but not at $6$.