I believe I can shed some light on this.
Whenever you load a gun with bullets (any gun that doesn't need a magazine or clip) the bullets now in the gun can be ejected and turn back into stackable bullets.
Any flare round you find is acting as if it is already in a gun when you find it on the ground and you can eject it even though it isn't in a gun, also you need to use that eject option on them if you wish to stack them with other flare rounds.
You shouldn't have to eject a flare round on the ground before you can stack it with other flare rounds and they should spawn with a number telling you how many flare rounds there are in the stack you found.