When you have 2 teleporters with units already orderd to move in the teleporter. If you then switch one of the teleporters on and connect it with a third teleporter then units pour trough. However if you then switch the destination teleporter with another teleporter (and the first on was still sending units) Then quite a large portion of that army that was entering the telporter has gone away into thin air... Don't think this is supposed to be...
are you sure? have you tested with no unit production on, so you can review the game looking at total units in army tab to see the number decrease. otherwise maybe they exited the teleporter they entered.