Free algebras provide an example:
Let $k$ be a field, and let $R=k\langle x,y\rangle$ be the free associative, unital $k$-algebra in two (non-commuting) indeterminates. Then every left and right ideal of $R$ is free, and so $R$ is necessarily hereditary on both sides. However, the right ideal $X$ generated by $x$ and the right ideal $Y$ generated by $y$ have zero intersection, since the elements of $X$ are precisely the $k$-linear combinations of monomials beginning with $x$ and the elements of $Y$ are precisely the $k$-linear combinations of monomials beginning with $y$; $R$ is a $k$-direct sum $k \oplus X \oplus Y$. If $S=R\setminus\\{0\\}$, then $xS \cap yR = (X \setminus \\{0\\}) \cap Y = (X \cap Y) \setminus \\{0\\} = \\{0\\} \setminus \\{0\\} = \varnothing$ so the set of non-zero-divisors of $R$ is not a right permutable set, and $R$ is not a right Ore domain (or a left Ore domain).