Let $\Sigma^\mathrm{ST}$ be a set of sentences that is valid in standard semantics and $\Sigma^\mathrm{Henk}$ be a set of sentences that is valid in Henkin semantics. Since $\Sigma^\mathrm{Henk}\subseteq \Sigma^\mathrm{ST}$ and $\Sigma^\mathrm{Henk}$ is r.e., but $\Sigma^\mathrm{ST}$ is not r.e. so there is a sentence $\sigma$ that is valid in standard semantics but is not valid in Henkin semantics.
However, there is a concrete example of such sentence? I think an analogue of Replacement $$ \forall X\forall f \exists Y \forall x : Y(x)\leftrightarrow X(f(x)) $$ (where $X$ and $Y$ are unary predicate symbol and $f$ is a unary function symbol) is a such sentence, but I don't know how to prove it. Thanks for any help.
For a very simple case of a sentence that is a valid on standard semantics and not in Henkin semantics (broadly understood), take the sentence
$$\exists X\forall x(Xx \equiv x \neq x)$$
which says that there is an empty property. That is valid on the standard semantics (since the quantifier $X$ over unary properties always ranges over all possible subsets of $D$ where $D$ is the domain of the first-order quantifier -- which always includes the empty subset). But it is not true in every Henkin model [since in Henkin models, the domain of the second-order quantifier is not constrained to included every possible subset of the the domain if the first-order quantifier.]
Which shows that not every instance of the comprehension scheme holds in Henkin models (broadly understood), though of course it does in full or standard models.
[The standard work on these matters is Stewart Shapiro's Foundations without Foundationalism: A Case for Second-Order Logic. A quick check confirms that your initial question is in fact answered on p. 89.]
Suppose however, to follow up Carl Mummert's observation, we restrict ourselves to so-called faithful Henkin models (models which don't falsify any instance of the usual second-order comprehension schema or falsify choice). Indeed, talk of Henkin models often just means such faithful models. Then we can refine the original question: what is an example of a second-order sentence which is valid on full semantics, but not on true in all faithful Henkin models?
Well, a fancy but quite cute example, assuming the continuum hypothesis is true, is the second-order sentence which formulates the continuum hypothesis which comes out true on the standard semantics, but which can fail in faithful Henkin models.
For a less exotic but perhaps more approachable example, see Carl Mummert's very helpful answer.
[Again, a quick check to confirm my increasingly fallible memory shows that I must have got that from Shapiro, p. 105. ]