Was the system worked on recently? A pocket of air will do that.
For a car that is stock, first thing is to crack open the bleed valve which is at the back passenger side of the super charger. You need a 10 mm and 7 mm combo wrenches. Put a rag under the valve just to catch the coolant that comes out. If there is air in the system, when you open the valve no coolant will come out for a few seconds, and then the coolant will come out. It won't spray all over, so don't worry about that. Just kind of runs out.
Maybe there's a leak in the system? If you get a vacuum fill tool and hook it up you should see 22 inches of vacuum or around there and it should hold at that reading for a minute or more. If it doesn't you have a leak somewhere. If it holds vacuum, then I'd run the vacuum tool while the pump/car is running. When I've done this, I use my tazer burnbox that has a cooldown mode so just the pump is running.