Thanks for testing it so thoroughly, that helped a lot! Found it: flyers placed by a player (like from the map editor) were never handled by the mod, so the airborne ones never landed and no turret could hit them. That's why exactly one of the three versions of each tier stayed untargetable in your test. Fixed in 0.0.9, including flyers already stuck that way in a save.
I couldn't reproduce it in a normal game though (all tiers landed fine to attack turrets, even walled ones). If you see a flyer in a regular game that stays untargetable, please send me the save and I'll look into it.