You can learn of Code violations in all kinds of ways, not just through formal inspections. For example, a contractor's rep tells you about a Code violation that one of the firm's electricians ran across incidentally while working at your facility.
Such impromptu inspections give you a chance to fix things before your insurance company discovers them and issues the typically ill-timed conformance notice. They also give you a chance to fix Code violations before they turn into reportable events, such as a fatal fire. Encourage such inspections by taking them seriously.
Nevertheless, don't respond to any inspection, formal or not, without a close look at the Code. Something that is a violation generally may not be one in your particular case.
This situation of the violation that isn't a violation typically occurs where a Code rule has several exceptions. An example is the rule that a service drop or lateral can supply only one set of service entrance conductors [230.40]. Typically, not allowing the exceptions results in needless expense but "exception rejection" can also reduce safety.