Hi flyaxa, good question. It's unlikely that what you're hearing is a "short runway." What you're hearing is probably part of an instruction to "hold short of runway 4L."
To avoid misinterpretation, all taxi routes including a runway must include language like "Taxi to runway ___ via taxiway ___" along with explicit instructions to cross (or not to cross) any runways that lie along the specified taxi route. Particularly at a busy, complex, or unfamiliar field, many pilots will pull up an airport diagram and follow along as they're given a taxi clearance.
At JFK, a possible taxi clearance might be "Taxi to 4L via A, K, hold short of 13R." Other times, a plane may be at the runway ready for takeoff, but there could be an arriving flight, so the tower will simply advise to "Hold short of 4L, traffic on short final" or similar.