"Without incident" means literally nothing remarkable happened. For example, if he had been behaving erratically or threatened suicide during the earlier flight, those would be incidents that should've tipped someone off that they should intervene and not let this guy back up.
If there had been an incident, further investigation would be warranted to determine if this was preventable, and if so, who could have prevented it. The journalist is specifically highlighting that no one but the pilot appears to be at fault right now.