I've just noticed this while working with a PR. I had a mix of old and new hashes due to git merge failure, i.e.: foo NNN BLAKE2B ... SHA512 ... === foo NNN SHA256 ... SHA512 ... WHIRLPOOL ... The call to 'repoman manifest' turned this into: foo NNN BLAKE2B ... SHA256 ... SHA512 ... WHIRLPOOL ... and afterwards repoman didn't want to remove the old hashes. This looks like the same problem eva@ hit (if I recall correctly).
repoman support has been removed per bug 835013. Please file a new bug (or, I suppose, reopen this one) if you feel this check is still applicable to pkgcheck and doesn't already exist.