There are a number of possible causes for this problem. They are, in no particular order:
You are not using the new make buildkernel and make installkernel targets, and your source tree is different from the one used to build the currently running system (e.g., you are compiling 4.3-RELEASE on a 4.0-RELEASE system). If you are attempting an upgrade, please read the /usr/src/UPDATING file, paying particular attention to the ``COMMON ITEMS'' section at the end.
You are using the new make buildkernel and make installkernel targets, but you failed to assert the completion of the make buildworld target. The make buildkernel target relies on files generated by the make buildworld target to complete its job correctly.
Even if you are trying to build FreeBSD-STABLE, it is possible that you fetched the source tree at a time when it was either being modified, or broken for other reasons; only releases are absolutely guaranteed to be buildable, although FreeBSD-STABLE builds fine the majority of the time. If you have not already done so, try re-fetching the source tree and see if the problem goes away. Try using a different server in case the one you are using is having problems.