EDIT: Let $M,N$ be compact connected smooth Riemannian manifolds. Let us assume that $N$ is closed, while $M$ might have a geodesically convex boundary.
Given $f\colon M\to N$ be an $\varepsilon$-almost Riemannian submersion, i.e. a submersion such that for any point $x\in M$ and any tangent vector $v\in T_xM$ which is orthogonal to the tangent space $T_xF$ to the fiber $F=f^{-1}(f(x))$ one has $$(1-\varepsilon)|v|\leq |df_x(v)|\leq (1+\varepsilon)|v|.$$
Assume in addition that the restriction $f|_{\partial M}\colon \partial M\to N$ is an $\varepsilon$-almost Riemannian submersion.
Let us denote by $D$ the maximal diameter of the fibers of $f$.
Question. Is it true that if $0\leq \varepsilon < 1/100$ and $D< inj(N)/100$ then the fibers of $f$ are connected?
Remark. I think I can prove this in two cases: (1) for $\varepsilon =0$, (2) for closed $M$ and small positive $\varepsilon$.