I don't understand your exact state. If you're just practicing, then dump your root partition again, or, recover it from /altroot if you use that.
A new system install will create an entire hierarchy, including /usr and /var. Depending on your specific filesystems that include OS-related files of all kinds, you could easily get out-of-sync without a great deal of care.
For example, packages usually place files in /usr/local and in /var, but they are not restricted to those, many put configuration files in /etc. In addition, the installed-package database is stored in /var/db/pkg/*, and needs to be kept in sync with /etc, /usr/local, and other /var components that packages create.
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