In sideview, both the Sword and the Stomp boots have screwy hit detection.
There are several instances in this quest of the sword passing through enemies when Link is in midair.
Also, the Stomp Boots only seem to work if Link jumps from below the level of the enemy.
Please look into this.
[816] Sideview Fliers Have Screwy Hit Detection
Why didn't you just say "flying enemies"? It's the key to this whole bug!
Okay... fixed. I think. Although there is a slight chance I made the hit detection a bit too generous.