When you're working on a migration, you may need to change the row IDs being used. If you do, the migrate map and message tables may no longer match and will cause you issues. To resolve this, you can drop the tables with sql queries and re-import.
These issues are for a better fix:
Provide a way to remove migration tables (ID map etc.)
https://www.drupal.org/project/drupal/issues/2713327
Provide a drush wrapper to destroy/delete migration tables
https://www.drupal.org/project/migrate_tools/issues/2997576
Expose full set of debugging data in migrate_message table (filterable/searchable)