One tends to run into non-conservativity of stalks when working with sheaves of categories with colimits. There are some remarks in the literature about this point, for sheaves valued in the $\infty$-category of presentable stable $\infty$-categories, see for instance https://arxiv.org/pdf/1704.04291 remark 2.8.2.
The $\infty$ is not really essential: we can adapt all that to get an example of a 1-category $\mathcal{A}$ which does the job. Namely, let $\mathcal{A}$ be the category whose objects are small posets with all joins, and whose morphisms are order preserving maps which commute with joins. It then turns out that for sheaves on $\mathbb{R}$ valued in $\mathcal{A}$, taking stalks does not detect isomorphisms.
Let $\mathcal{F}$ be the $\mathcal{A}$-valued sheaf on $\mathbb{R}$ which assigns to each open set $U$ the poset of open subsets of $U$, where for each pair of opens $U \subseteq V$ the restriction $i_{U, V}^*: \mathcal{F}(V) \rightarrow \mathcal{F}(U)$ is given by intersection with $U$. Let $\mathcal{G}$ be the subsheaf of $\mathcal{F}$ which sends each open set $U$ to the poset of open subsets of $U$ which are unions of connected components of $U$. I claim that the inclusion $\mathcal{G} \rightarrow \mathcal{F}$ induces an isomorphism in stalks.
Fix a point $x$ in $\mathbb{R}$. Then the stalk of $\mathcal{G}$ at $x$ can be computed as the colimit of $\mathcal{G}((x-\varepsilon, x+\varepsilon))$ over all $\varepsilon > 0$. This is a constant diagram with value given by the poset $\lbrace 0 < 1 \rbrace$, so the stalk $\mathcal{G}_x$ is given by $\lbrace 0 < 1 \rbrace$.
General results about colimits of locally presentable categories imply that the stalk of $\mathcal{F}$ at $x$ can be computed as the limit $\lim_{U} \mathcal{F}(U)$, where once again we index over all neighborhoods of $x$, but where for each inclusion $U \subseteq V$ the transition in the diagram is given by the morphism of posets $(i_{U, V})_*: \mathcal{F}(U) \rightarrow \mathcal{F}(V)$ which is right adjoint to $i_{U, V}^*$. The maps $(i_{U, V})_*$ are all fully faithful, and hence the stalk of $\mathcal{F}$ at $x$ can be computed as the intersection of the images of $(i_{U, \mathbb{R}})_*$ over all neighborhoods $U$ of $x$. An open subset $W$ of $\mathbb{R}$ in the image of $(i_{U, \mathbb{R}})_*$ necessarily contains the complement of $U$, so we see that the intersection of all these images consists of at most two elements, namely $\mathbb{R}$ and $\mathbb{R}-\lbrace x \rbrace$. Both are realized: for any $U$ we have that $\mathbb{R} = (i_{U, \mathbb{R}})_*(U)$, while $\mathbb{R} - \lbrace x \rbrace = (i_{U, \mathbb{R}})_*(U - \lbrace x \rbrace)$. It follows that the stalk of $\mathcal{F}$ at $x$ is also given by the poset $\lbrace 0 < 1 \rbrace$.
We now have that the stalk of both $\mathcal{G}$ and $\mathcal{F}$ at $x$ is given by $\lbrace 0 < 1 \rbrace$. The morphism $\mathcal{G}_x \rightarrow \mathcal{F}_x$ preserves minimum elements since it is a morphism in $\mathcal{A}$. The only thing left to observe is that the morphism $\mathcal{G}_x \rightarrow \mathcal{F}_x$ is not constant. If it were, one would be able to conclude that the maps $\mathcal{F}(U) \rightarrow \mathcal{F}_x$ are all constant, since they would send both $U$ and the empty set to the same element. But this cannot happen, since the image of the maps $\mathcal{F}(U) \rightarrow \mathcal{F}_x$ should generate the target under joins.
This particular $\mathcal{A}$ is not locally presentable, however one can also find a locally presentable example by working with the category $\mathcal{A}'$ of small posets with countable joins and countable join preserving morphisms. The morphism of $\mathcal{A}$-valued sheaves $\mathcal{G} \rightarrow \mathcal{F}$ from above can also be regarded as a morphism of $\mathcal{A}'$ valued sheaves, and it turns out that the stalks in this setting are still given by $\lbrace 0 , 1 \rbrace$: this can be deduced from the case of $\mathcal{A}$ by using the fact that for every $U$ the posets $\mathcal{F}(U)$ and $\mathcal{G}(U)$ are equal to their own $\operatorname{Ind}_{\omega_1}$-completion.