rpm-ostree (just like any image system, including Docker and cloud images) is subject to uid/gid drift. In both of the latter, it's possible to use "yum update", which works as well as it always has. However, for rpm-ostree, they must be allocated consistently on the server side. https://git.fedorahosted.org/cgit/fedora-atomic.git/commit/?id=debbecbc6cec7ae494f26703d0ae28b2c53b0e26 is a commit for master and f22 that must now be backported to f21, because the most recent update changed uids for important things like "sshkeys".
rpm-ostree-2015.3-1.fc21 has been submitted as an update for Fedora 21. https://admin.fedoraproject.org/updates/rpm-ostree-2015.3-1.fc21
Package ostree-2015.3-2.fc21, libgsystem-2015.1-1.fc21, rpm-ostree-2015.3-2.fc21: * should fix your issue, * was pushed to the Fedora 21 testing repository, * should be available at your local mirror within two days. Update it with: # su -c 'yum update --enablerepo=updates-testing ostree-2015.3-2.fc21 libgsystem-2015.1-1.fc21 rpm-ostree-2015.3-2.fc21' as soon as you are able to. Please go to the following url: https://admin.fedoraproject.org/updates/FEDORA-2015-4164/rpm-ostree-2015.3-1.fc21,ostree-2015.3-2.fc21,libgsystem-2015.1-1.fc21 then log in and leave karma (feedback).
ostree-2015.3-2.fc21, libgsystem-2015.1-1.fc21, rpm-ostree-2015.3-2.fc21 has been pushed to the Fedora 21 stable repository. If problems still persist, please make note of it in this bug report.