That's what the permitting process is (theoretically) for: to ensure specific, potentially dangerous repairs and construction are done according to safety code.

Hypothetical situation: If you have to get a permit to do general contractor work, and the hole you find violates code, I would assume you would be expected to repair the hole. depending on the size of the hole (are we talking pinholes? Nails? How do you mount shit to a stud on a wall built out of haybales? Is the stud buried in the bale or extra thick to accommodate the thicker wall? I've never worked with one of these hay walls, the idea of them is so neat) I'd talk to the owner specifically about how I was repairing it so they could repair any other holes themselves, as that would likely not be the job I was hired to do. I haven't worked construction since high school tho so ymmv.