$\def\rank{\operatorname{rank}}
\def\null{\operatorname{null}}
\def\ker{\operatorname{Ker}}
\def\im{\operatorname{Im}}$The answer is yes: exactness in the bundles implies exactness in the sheaves of sections. Actually, we have exactness on sections, see Proposition 8 below.
Definition 1. Let $\varphi:E\to F$ be a morphism of vector bundles over $M$. We say that $\varphi$ has locally constant rank if every point in $M$ has an open neighborhood $U$ such that $\rank\varphi_p=\rank\varphi_q$ for all $p,q\in U$.
Lemma 2. Let $\varphi:E\to F$ be a vector bundle homomorphism over $M$. The function
\begin{align*}
M&\to\mathbb{N}\\
p&\mapsto\rank\varphi_p
\end{align*}
is lower semicontinuous.
Proof. Consider the matrix of $\varphi$ with respect to two local frames of $E$ and $F$ and apply this. $\square$
Lemma 3. Suppose $E\xrightarrow{\varphi} F\xrightarrow{\psi} G$ is an exact sequence of smooth vector bundles over a smooth manifold $M$ (by definition, this means that the sequence is fiberwise exact). Then $\varphi$ and $\psi$ have locally constant rank.
Proof. Call $\null\psi,\rank\varphi:M\to\mathbb{N}$ to the functions $p\mapsto\null\psi_p,\rank\varphi_p$. Since $\rank\varphi=\null\psi=\rank F-\rank\psi$, it suffices to show that one of $\varphi$ or $\psi$ has locally constant rank. Let $p_0\in M$. Since $\rank\varphi,\rank\psi$ are lower semicontinuous functions (Lemma 2), there is an open neighborhood $U\subset M$ of $p_0$ such that for all $p\in U$,
\begin{align*}
\rank\varphi_p&\geq\rank\varphi_{p_0}\\
&=\null\psi_{p_0}\\
&=\rank F-\rank\psi_{p_0}\\
&\geq\rank F-\rank\psi_p\\
&=\null\psi_p\\
&=\rank\varphi_p.
\end{align*}
Hence, all “$\geq$” are actual equalities, so $\varphi|_U$ has constant rank. $\square$
Lemma 4. Let $\varphi:E\to F$ be a smooth vector bundle homomorphism over $M$ with locally constant rank. Then the subsets $\ker\varphi\subset E$, $\im\varphi\subset F$, which fiberwise are given by the kernel and the image of the map on fibers, are smooth subbundles of $E$ and $F$.
Lemma 4 is Theorem 10.34 of J.M.Lee, Introduction to Smooth Manifolds, 2nd ed., so we redirect the reader there to see the proof.
Given a morphism of vector bundles $\varphi:E\to F$ over $M$, we denote $\Sigma_\varphi$ to the induced morphism on sheaves of sections $\Sigma_E\to\Sigma_F$.
Lemma 5. Let $\varphi:E\to F$ be a vector bundle homomorphism with locally constant rank. Then $\ker\Sigma_\varphi=\Sigma_{\ker\varphi}$, $\im\Sigma_\varphi=\Sigma_{\im\varphi}$ as sheaves.
Proof. The equality $\ker\Sigma_\varphi=\Sigma_{\ker\varphi}$ is easy to show.
We are going to show that the image presheaf of $\Sigma_\varphi$ equals $\Sigma_{\im\varphi}$. That is, for $U\subset M$ be open, we will show that $\im(\Sigma_{\varphi,U})=\Sigma_{\im\varphi}(U)$. The containment $(\subset)$ is easy, so we show the converse. Let $\sigma\in\Sigma_{\im\varphi}(U)$. By the proof of the aforementioned theorem 10.34 of Lee's book, there is an open cover $U=\bigcup_iU_i$ and local sections $\tau_i\in\Sigma_E(U_i)$ such that $\varphi\circ\tau_i=\sigma|_{U_i}$ for all $i$. Let $\{\rho_i\}$ be a partition of unity on $U$ subordinated to the open cover $\{U_i\}$. Then we can define $\tau=\sum\rho_i\tau_i$, which is a local section of $E$ over $U$. This way,
\begin{align*}
\varphi\circ\tau
&=\varphi\circ\left(\sum\rho_i\tau_i\right)\\
&=\sum\varphi\circ(\rho_i\tau_i)\\
&=\sum\rho_i(\varphi\circ\tau_i)\\
&=\sum\rho_i\sigma|_{U_i}\\
&=\sum\rho_i\sigma\\
&=\left(\sum\rho_i\right)\sigma\\
&=\sigma.
\end{align*}
Hence, $\sigma\in\im(\Sigma_{\varphi,U})$. $\square$
Lemma 6. Let $\varphi:E\to F$ be a morphism of smooth vector bundles over $M$. Then the image presheaf of $\Sigma_\varphi$ is a sheaf.
Proof. The image presheaf is a separated presheaf for it is a subpresheaf of a sheaf (namely, $\Sigma_F$). It is left to verify the gluing axiom. Let $U\subset M$ be open and let $U=\bigcup_{i\in I}U_i$ be an open cover. Let $\tau_i\in\Sigma_E(U_i)$ and suppose that the sections $\sigma_i=\varphi\circ \tau_i$ satisfy $\sigma_i|_{U_i\cap U_j}=\sigma_j|_{U_i\cap U_j}$. Let $\rho_i$ be a partition of unity on $U$ subordinated to $\{U_i\}$. Then $\tau=\sum\rho_i\sigma_i$ is a smooth local section of $E$ and $\varphi\circ\tau=\sum_i\rho_i\sigma_i$. Let $j\in I$ and pick $p\in U_j$. We have
\begin{align*}
(\varphi\circ\tau)(p)
&=\sum_i(\rho_i\sigma_i)(p)\\
&=\sum_{\substack{i\in I\\p\in U_i}}(\rho_i\sigma_i)(p)\\
&=\sum_{\substack{i\in I\\p\in U_i}}\rho_i(p)\sigma_i(p)\\
&=\sum_{\substack{i\in I\\p\in U_i}}\rho_i(p)\sigma_j(p)\\
&=\sum_{i\in I}\rho_i(p)\sigma_j(p)\\
&=\left(\sum_{i\in I}\rho_i(p)\right)\sigma_j(p)\\
&=\sigma_j(p).
\end{align*}
Hence, $\varphi\circ\tau|_{U_j}=\sigma_j$. $\square$
Remark 7. Behind Lemma 6 there is a more general phenomenon. To explain it, we make the following definitions: a sheaf of rings $\mathcal{O}$ over a topological space $X$ is said to be to be fine if it has partitions of unity. This is, for all open subsets $U\subset X$ and all open covers $U=\bigcup_{i\in I} U_i$, there are sections $\rho_i\in\mathcal{O}(U)$, $i\in I$, such that $\{\operatorname{supp}\rho_i\}_{i\in I}$ is a locally finite family of subsets of $U$ and $\sum_{i\in I}\rho_i=1$. The previous lemma generalizes to: if $\varphi:\mathcal{F}\to\mathcal{G}$ is a morphism of $\mathcal{O}$-modules and $\mathcal{O}$ is fine, then the image presheaf of $\varphi$ is already a sheaf. The proof is formally the same, but now instead of evaluating at $p$, one takes stalks at $x$.
Proposition 8. Let $E\xrightarrow{\varphi} F\xrightarrow{\psi} G$ be a sequence of smooth vector bundles over $M$. Then exactness of $E\to F\to G$ implies exactness of $\Sigma_E\to\Sigma_F\to\Sigma_G$, but the converse doesn't hold in general. Furthermore, $\Sigma_E\to\Sigma_F\to\Sigma_G$ is exact if and only if for all open subsets $U\subset M$, the sequence $\Sigma_E(U)\to\Sigma_F(U)\to\Sigma_G(U)$ is exact.
Proof. The converse is shown not to hold in the comment I wrote to my question. Suppose first that $E\to F\to G$ is exact. By Lemma 3, both $\varphi$ and $\psi$ have locally constant rank. By Lemma 4, $\im\varphi$ and $\ker\psi$ are smooth subbundles, and they are equal by hypothesis. By Lemma 5, we have $\ker\Sigma_\psi=\Sigma_{\ker\psi}=\Sigma_{\im\varphi}=\im\Sigma_\varphi$. This means exactness of the sequence of sheaves $\Sigma_E\to\Sigma_F\to\Sigma_G$.
The fact that “$\Sigma_E(U)\to\Sigma_F(U)\to\Sigma_G(U)$ is exact for all open $U\subset M$” implies “$\Sigma_E\to\Sigma_F\to\Sigma_G$ is exact” is a general property of sheaves of abelian groups over a topological space: since filtered colimits are exact, we get that $\Sigma_{E,p}\to\Sigma_{F,p}\to\Sigma_{G,p}$ is exact. Conversely, suppose $\Sigma_E\to\Sigma_F\to\Sigma_G$ is exact, i.e., it holds $\ker\Sigma_\varphi=\im\Sigma_\varphi$. Then, for $U\subset M$ we have $\ker\Sigma_{\varphi,U}=\ker\Sigma_\varphi(U)=\im\Sigma_\varphi(U)=\im\Sigma_{\varphi,U}$, where in the last step we have applied Lemma 6. This means that $\Sigma_E(U)\to\Sigma_F(U)\to\Sigma_G(U)$ is exact. $\square$
With the definitions of Remark 7, the second part of Proposition 8 generalizes to: Let $(X,\mathcal{O}_X)$ be a ringed space such that $\mathcal{O}_X$ is fine, then the global sections functor $\Gamma(X,-):\mathsf{Mod}(\mathcal{O}_X)\to\mathsf{Mod}(\Gamma(X,\mathcal{O}_X))$ is exact (in other words, all sheaves of $\mathcal{O}_X$-modules are acyclic). The proof is done in the same way, now with the generalization of Lemma 6 explained in Remark 7.