"directory not empty", "no such file or directory" errors on upgrade

[Gary Aitken]

Upgrading from 11.2-RELEASE to 11.3-RELEASE

The final invoke of freebsd-update install completed with the following
messages:

///usr/src/sys/pc98/include/acpica_machdep.h  no such file or directory
rmdir: ///usr/src/contrib/ofed/usr.lib        directory not empty
rmdir: ///usr/src/contrib/ofed/usr.bin        directory not empty
rmdir: ///usr/src/contrib/llvm/tools/lldb/source/Plugins/InstrumentationRuntime/ThreadSanitizer   directory not empty
rmdir: ///usr/src/contrib/llvm/tools/lldb/source/Plugins/InstrumentationRuntime/AddressSanitizer  directory not empty

The upgraded system has no
   /usr/src/sys/pc98/  directory

The files in
   /usr/src/contrib/ofed/usr.lib
   /usr/src/contrib/ofed/usr.bin
   /usr/src/contrib/llvm/tools/lldb/source/Plugins/InstrumentationRuntime/ThreadSanitizer
   /usr/src/contrib/llvm/tools/lldb/source/Plugins/InstrumentationRuntime/AddressSanitizer

appear to be old versions left over from the original 11.2 install

Hints on the proper way to fix this?
(The system appears to be running ok so far, I presume because these are
source files and not binaries)

Thanks,

Gary