This bug has been around awhile. I did find #40322 but it's marked fixed. Well it isn't. It keeps coming back. I merged ntp recently, when I did man ntpd as a user I get: rm: remove write-protected regular empty file `/var/cache/man/cat1/ntpd.1.bz2'? I've been getting this routinely and have bugged it. One fix was to manually change permissions. That works fine once but it keeps happening over and over. Is the ebuild broken - are permissions getting set incorrectly by an install?
Can second that. This is fixable only by running bzip2recover as root.
Bug 40322 has a procedure to rm a directory, then emerge man. Does that work for you? Even if it does it's not a fix. I can do that, things work good then at some merge later it breaks again.
*** This bug has been marked as a duplicate of 40322 ***