When doing a pre-migration check or copying a site, the following message is displayed:

The term set used in the navigation settings cannot be found in the destination site.

The message is displayed when the term set used by the navigation settings of your source site is missing at your destination site (because it was not successfully migrated). For example, if your source site's navigation is driven by a term set called "My Term Set", this error means that "My Term Set" was not successfully migrated.

Migrate the term set from your source site to your destination site.

In the above example, "My Term Set" should be migrated to the destination. You can find more information about how to migrate term sets with ShareGate Migrate here.