Aye, there are a few dragon towers where it is possible to get into an aerial battle with flying opponents. However (despite what the story dialogue says) in reality it is only your party that will get targeted (although I believe the spell operates as Fireball, so being hit can actually also damage close enemies).
*Slight spoiler below*
Once you complete the Tower Keys quest, the story dialogue is again that the towers should now recognise & only attack flying "monsters" (ie anything not you), but again in reality what happens is the towers are basically turned off & no longer attack anything. Guess the distinction was too hard to programme in 1998
