I also noticed some directories having their ownership set to my user, which caused VirtualBox to complain.
If you can't wait for repositories to be updated, I think you can edit a config file. For example, I edited /usr/local/etc/pkg/repos/pcbsd.conf like so:
< signature_type: "fingerprints",
< fingerprints: "/usr/local/etc/pkg/fingerprints/pcbsd",
> signature_type: "pubkey",
> pubkey: "/usr/local/etc/pkg-pubkey.cert",
This makes it resemble the old version of the same file.