You are looking the the 5th meaning:

>at some point or degree before a goal or limit aimed at: _the shells fell short_ 

The 4th meaning does not apply here if the plane did not actually reach the runway. 
The plane of course stopped short too, but that was when it hit the rocks instead of the strip they landed short of 


>[Private plane lands short of Charlotte runway](http://www.charlotteobserver.com/2013/05/24/4061744/private-plane-lands-short-of-charlotte.html)