I guess that isomorphic means diffeomorphic. Let me provide an example that seems conceptually different from the others given so far.
Take $M= \mathbb{R}^4 \times \mathbb{R}^4_{\operatorname{ex}} \times \mathbb{R}$, where $\mathbb{R}^4_{\operatorname{ex}}$ is any exotic $\mathbb{R}^4$.
You have two projections
$$ p_1 \colon M \longrightarrow \mathbb{R}^4, \quad p_2 \colon M \longrightarrow \mathbb{R}^4_{\operatorname{ex}},$$
whose fibres are diffeomorphic to $\mathbb{R}^4 \times \mathbb{R}_{\operatorname{ex}}$ and $\mathbb{R}^4 \times \mathbb{R}$, respectively.
Since there exists no exotic $\mathbb{R}^5$, these fibres are both diffeomorphic to $\mathbb{R}^4 \times \mathbb{R}$, but the bases are not diffeomorphic.