Some people say to put 5 qts. of ATF when doing the filter change on my jetta 2001, some say to use only 4 qts. what is the correct amount needed?
The 4 speed automatic transmission in that era of Jetta is an "01M"- total fluid capacity is 5.3 liters but for a simple fluid and filter change (as opposed to a complete flush) you only need 3 - 3.75l (as it won't drain completely)
To add to motosubatsu's correct answer, the most likely reason is that there's probably almost a liter "trapped" in bottom of the torque converter.
Most converters have a plug, which can be accessed [usually] by removing a sheet metal plate and rotating the converter to the correct position to remove the plug and drain.
You then put in about 4 liters, start the vehicle so that the pump refills the torque converter, and add another liter. This is the correct way for a "proper job", but often it isn't done because it can be a real pain to accomplish this extra step.
I would never add the "capacity", as the 300 milliliters is likely "stuck" to various internal parts, depressions, trapped in the servos or valve body, etc. The design capacity is a so-called "factory fill" which assumes a bone dry new or rebuilt transmission with no residual ATF.
In any case, the dipstick will tell you where to top up to when checked properly - which varies from vehicle to vehicle.
Some are checked hot, some cold, idling in neutral/park, or engine off. The owner's manual or an online resource should yield the correct procedure. It's very important this procedure is followed exactly, as idling while running yields a lower dipstick level than parked, off, and cold (the fluid is pumped and flung all over the place, very dynamic). This can result in an underfill/overfill if you top up while not using the factory procedure.
Some dipsticks have multiple check points, and some even have the check procedure engraved into the dipstick blade. And some have no dipstick whatsoever, and some even claim to have "lifetime" fluid. Those you gotta love. (Maybe they meant my lifetime...) [sigh]