"pkg clean" is removing everything from the cache directory.
"pkg clean" (without any option/argument) removes packages that have been superseded by newer versions, and any packages that are no longer provided. Moreover, in order to remove all the packages from the cache, "pkg clean -a" is used. However, it is observed that even without giving an "-a" option, "pkg clean" is deleting all cached packages including those, which have not been superseded by newer versions yet and are still in use.
Yes, I can confirm this. "pkg clean -n" also shows the full set.
I created https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=249917 some time ago. It's a good thing more people are experiencing this odd behaviour, and hopefully it will be fixed.