I don't remember seeing any little blue "Flying" status effect icon on him. But what the page about Ghostwalking seems to say, surprisingly enough, is that that isn't a bug.You cannot attack flying opponents with close-combat attacks unless you are flying!
That same page, however (https://wiki.nexusclash.com/wiki/Ghostwalk) says it definitely IS a bug that my pets weren't leaping at him.
I still had four left; he seemed to realize they weren't retaliating after he killed the first one, and decided to take advantage of that to start pelting us with teeth instead.
Theoretically, it's possible that he had a potion of flying on him (though he didn't have Draught of Discretion) and the bug is instead with that status effect not showing up. But... given how he didn't seem to realize at first that the pets weren't a threat, it doesn't seem like it.