The only incident I have ever heard of was not one could have ever considered close to a hijacking.
It happened to company airplane of a friend of mine, years before 9/11. They were waiting for the boss to show up and when he did they walked out to the airplane (Falcon 50) and lo and behold there was someone sitting in the cabin. They first thought that this guy had just gotten into the wrong airplane. No this guy wanted to go for a ride. They called the cops and off he went. Turned out he was a mental patient. This happened in the early 80s.
The above incident really started security awareness within corporate aviation.