As far as I know, it isn't really a bug with the replay, just an oddity with the animation. When a unit is moved, it gets there pretty much instantly, but the movement animation takes a little while to catch up. Thus, a player can order a transport to move, select the spot where he ordered it to (which LOOKS empty), then pick a unit inside and have it disembark, all before the transport's movement animation is done. You should try it sometime if you really want to see it for yourself.
On the other hand, not being a dev, I could be completely wrong, but that's what it looks like to me