There are non-separable zero-dimensional compact Hausdorff spaces with a separable superextension.
Because of zero-dimensionality one obtains $\lambda X$ as the space of all maximal linked systems of clopen sets.
In order that $\lambda X$ be separable it is necessary and sufficient that the Boolean algebra of clopen sets is $\sigma$-linked: extend each of the countaly many linked systems to a maximal one, the resulting countable set is dense in $\lambda X$.
In order that $X$ itself is not separable it is necessary and sufficient that the Boolean algebra of clopen sets is not $\sigma$-centered.
The measure algebra on $[0,1]$ is $\sigma$-linked, but not $\sigma$-centered. Hence its Stone space is a counterexample.
Other examples were constructed by Murray Bell in Two Boolean Algebras with Extreme Cellular and Compactness Properties (Canadian Journal of Mathematics, Volume 35, Issue 5, 01 October 1983, pp. 824-838). For example a Boolean algebra that is $\sigma$-linked, but not $\sigma$-$3$-linked. These have the advantage that they are subalgebras of $\mathcal{P}(\omega)/\mathit{fin}$; hence their Stone spaces provide examples that are even remainders in compactifications of $\mathbb{N}$. The measure algebra need not be embeddable in that algebra. Thanks to Jan van Mill for this reference.