The category of schemes is not small-concrete.
Let $S$ be a generating set. Let $U$ be the set of all rings $A \neq 0$ such that $\mathrm{Spec}(A)$ is an open subscheme of a scheme in $S$. Let $X$ be a set whose cardinality is larger than any element of $U$, for example, $2^{\bigsqcup_{A \in U} A}$. Let $K$ be the field $\mathbb{Q}(t_x)_{x \in X}$, where $t_x$ are a collection of algebraically independent generators indexed by $X$. So $|K|$ is larger than $|A|$ for any $A \in U$. Since ring maps from a field to a nontrivial ring are always injective, $\mathrm{Hom}(\mathrm{Spec}(A),\mathrm{Spec}(K))=\emptyset$ for every $A \in U$, and therefore $\mathrm{Hom}(s,\mathrm{Spec}(K))=\emptyset$ for every $s \in S$.
There is only one map from the empty set to itself. But $\mathrm{Spec}(K)$ has nontrivial isomorphisms, coming from permuting the generators. So
$\mathrm{Hom}(\mathrm{Spec}(K),\mathrm{Spec}(K)) \longrightarrow \mathrm{Hom}_{\mathrm{Set}^{S^\mathrm{op}}}( (\mathrm{Spec}(K))(-), (\mathrm{Spec}(K))(-))$
is not injective.
