This isn’t an issue as this isn’t exclusive to the nav nestable element (some are prefixed with brxe- and others with brx-).
As for the .menu-item class, I agree it might be better to include a prefix to avoid any conflicts. Though I think this is an improvement and not a bug.
Your right probably more of an improvement but these type of issues are better to catch early on since they are breaking changes for those that target the actual classes (which is why I thought of them as more as a bug).