Do you restrict repository deletion?

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To avoid this, the organisation owners should be the only members allowed to delete repositories. Follow these instructions:

1. Go to your organisation | Settings | Member privileges.
2. Under 'Repository deletion and transfer', ensure 'Allow members to delete or transfer repositories for this organization' is deselected
3. Save

See GitHub docs Setting permissions for deleting or transferring repositories

This will ensure that even Admin users cannot accidentally delete or transfer repositories