No... you should always fill through the reservoir. Just know that when you fill the reservoir to the line the system is not necessarily full. Fill it up and let the engine warm up and circulate the coolant. If the level goes back down, fill it up again.
It is possible you have a slow coolant leak somewhere and just got down to a very low level. If you have had it flushed and refilled, just keep an eye on it and see if it creeps down again... watch for wet spots under the car too.