What is the goal of the quality/safety system? Prevent bad product from 1. being created, and 2., if #1 somehow fails, prevent bad product from leaving the facility. To that end, the system does not care who or under what circumstances a nonconformance is identified. In my opinion, even an outside contractor fixing the lights should have the authority to report a nonconformance they observe.
Each system and each company is a little different. If I were the internal auditor in question, I would maintain the scope of the audit but report the nonconformance preferably on a separate Corrective Action report or whatever is in your system. I might even note it on my audit report, but only briefly and move on. One of the last things you want in your internal audit program, in my opinion, are audits that do not maintain the scope and go off in all different directions. For one, if the audit goes off in other directions, is the laboratory in this example getting a fair and sufficiently thorough audit? Another reason is when a future auditor reviews the previous audit(s) they need a focused report to help them effectively evaluate the state of the laboratory at the time of the last audit so their current audit (with follow-ups) can be effective and focused.