The agency overseeing the troubled $9.2-billion Honolulu light-rail project frequently overpaid its contractors, including HDR Engineering Inc., the primary construction management consultant, according to a recently released state audit. Though based on a small sample of invoices, the assessment of the Honolulu Authority for Rapid Transportation’s administrative practices found examples of insufficient documentation, use of incorrect billing rates and misinterpretation of opportunities to realize some $124,000 from contractors. Already six years late and nearly double its original estimate, the project is also the subject of a federal investigation into construction-contract and change-order management.