THIS !
One cannot hit many flying enemies, sometimes you hit by chance, when shooting next to them, but ON TARGET your arrow passes through them.
One can however damage those enemies with AOE skills (like evasion)

This bug was not encountered in the last early access version of the game.

I have noticed this also. Its a much smaller hitbox on some flying mobs. The hitbox is located underneath the mobs in question and unless you are using AoE your character tend to be running around in circle on the mob if your melee to try and find the tiny hitbox.

Exactly, sometimes if you randomly target this offset hitbox, the enemy 'blinks' in red (as it normally would) - in those short moments it can be hit, more by chance than deliberately.

This seems to be a calibration issue. When I run away and the enemy resets (returns to its spawn position), there's a good chance that it has a normal hitbox again, when I encounter it again.