To compare $\mathrm{Ext}^1(E,F)$ to $\mathrm{Ext}^1(i_*E,i_*F)$ one can proceed as follows. First, there is adjunction isomorphism
$$
\mathrm{Ext}^\bullet(i_*E,i_*F) \cong \mathrm{Ext}^\bullet(Li^*i_*E,F).
$$
Next, since $i$ is an embedding of a Cartier divisor, there is a distinguished triangle
$$
Li^*i_*E \to E \to E(-C)[2],
$$
where $E(-C) = E \otimes \mathcal{O}_C(-C)$. Applying the functor $\mathrm{Ext}^\bullet(-,F)$ to this triangle, we obtain a long exact sequence
$$
\dots \to \mathrm{Ext}^{i-2}(E(-C),F) \to \mathrm{Ext}^{i}(E,F) \to \mathrm{Ext}^{i}(Li^*i_*E,F) \to \mathrm{Ext}^{i-1}(E(-C),F) \to \dots
$$
Since $\mathrm{Ext}^i(-,-)$ between two sheaves vanishes for $i \not\in \{0,1,2\}$, using the above adjunction isomorphisms, we obtain an isomorphism
$$
\mathrm{Hom}(E,F) \to \mathrm{Hom}(i_*E,i_*F),
$$
a short exact sequence
$$
0 \to \mathrm{Ext}^{1}(E,F) \to \mathrm{Ext}^{1}(i_*E,i_*F) \to \mathrm{Hom}(E(-C),F) \to 0
$$
and yet another isomorphism
$$
\mathrm{Ext}^{2}(i_*E,i_*F) \to \mathrm{Ext}^1(E(-C),F).
$$
In particular, the morphism $\mathrm{Ext}^{1}(E,F) \to \mathrm{Ext}^{1}(i_*E,i_*F)$ is an isomorphism if and only if $\mathrm{Hom}(E(-C),F) = 0$.