From the Changelog notes:
"Warnings may be generated if the destination filesystem doesn't permit chown() or chmod() system calls to be made on files — for example, if the destination filesystem is a FAT filesystem."
More explicitly, rename() may still return (bool) true, despite the warnings that result from the underlying calls to chown() or chmod(). This behavior can be misleading absent a deeper understanding of the underlying mechanics. To rename across filesystems, PHP "fakes it" by calling copy(), unlink(), chown(), and chmod() (not necessarily in that order). See PHP bug #50676 for more information.
On UNIX-like operating systems, filesystems may be mounted with an explicit uid and/or gid (for example, with mount options "uid=someuser,gid=somegroup"). Attempting to call rename() with such a destination filesystem will cause an "Operation not permitted" warning, even though the file is indeed renamed and rename() returns (bool) true.
This is not a bug. Either handle the warning as is appropriate to your use-case, or call copy() and then unlink(), which will avoid the doomed calls to chown() and chmod(), thereby eliminating the warning.