In aerial battle it nearly cannot be done (although I managed to make it once or maybe twice, it was a sheer luck). If fighting walking monsters from the air, you can do it if you 1) do your battle reasonably near to the tower; 2) fly just above the ground. Then the fireballs will hit the ground where you are flying and this way some hits can be scored.I'd bet it wasn't very hard to discern. This is the way I see it: there is a big difference between the party and the monsters -- they use another data structures, and are stored completely differently one from the another. It is not hard to check whether the party is flying and to send a fireball towards its position if it truly is.
Monsters, on the other hand, are probably in some kind of array, separated from the party. So you need to iterate over all monsters, check whether they are flying, if they are, calculate their distance from the tower and choose the nearest one. Then shoot a fireball at it. I don't recall when MM6 was released -- 1996? Or 1997? Maybe the programmers didn't dare to lay another burden on "weak" computers working already at their full? Who knows today ...
