When you drain the transmission from the plug, you aren't getting the entire contents out of the transmission, there will be some fluid still in the torque converter and other internal parts. Don't get me wrong though, you're not supposed to run these when they are low. When the engine runs, it drives the transmission fluid pump as well no matter what gear you're in. What I would do is fill the transmission (if you haven't done it already) then drain it again, this time catch the fluid and strain it through a coffee filter and look for any debris. When you start seeing grits and sparkly bits, there is a problem. If there is little to none then I wouldn't worry too much, at that point refill it to the specified level and drive as normal.