freebsd-update tends to only work with binaries as they were installed from the CD, and with the GENERIC kernel. If you have manually rebuilt the world at any point, I believe freebsd-update will fail. Same if you have a non-GENERIC kernel.
You also don't mention what happened during the update. What kind of log output was generated? Were there any error? Did it mention the kernel as being installed and to be updated?
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