They also store a train on track 5 at wtc, and the stretch between journal square and near the portal is also used for storage, i believe that section has 3 tracks intended for both work & shop movements/storage as well as this operational pattern of storage. There is also layovers overnight & weekends etc at hoboken and 33rd street. During the day, especially peak hours, very frequently only shopped cars will be seen or trains with a problem that were taken out mid cycle. Take a train from newark to hoboken via jsq overnight and you will see a lot more trains/cars parked in those yard areas and in the stations. In fact frequently they will park a train upstairs at newark during "off hours" and only use the lower track.
Next stop the square, journal square station next!