This question says that the theory ZFC + $0^\#$ has incomparable minimal transitive models. It proves this as follows (my emphasis):
[F]or every c.e. $T⊢\text{ZFC\P}+0^\#$ having a model $M$ with $On^M = α < ω_1$, the intersection of all such $M$ equals $L_α$, and furthermore a subset of $L_α$ is definable (with parameters) in all such $M$ iff it is in $L_{α^{+,\mathrm{CK}}}$. To see this (briefly), $0^\#$ allows $M$ to 'continue' $L$ beyond $α$, and $L_{α^{+,\mathrm{CK}}}⊆(L_{α^{+,\mathrm{CK}}})^M$ (the well-founded part of any model of KP being admissible), and so $L_{α^{+,\mathrm{CK}}}∩V_α=L_α$. Also, existence of $M$ is $Σ^1_1(α)$, so the intersection of all $M$ is at most $L_{α^{+,\mathrm{CK}}}$.
The bolded part uses Mostowski's absoluteness theorem. But to use Mostowski's absoluteness theorem we need $L_{α^{++,\mathrm{CK}}}$ to see that $\alpha$ is countable, and I have no idea how to prove that.
I originally posted this question on Stackexchange but two comments recommended moving it to MathOverflow.