The combo-layer utility ought to update the commit hash to the merge commit otherwise in next call it will end doing a format-patch from the commit just before the merge and trying to reapply already commited ones.
This should finally be resolved by the following fix: http://git.yoctoproject.org/cgit/cgit.cgi/poky/commit/?id=dcb8f89723f809ceee9dbb0941a2cc5a43400e99