Wish-Ender has been inconsistent since SoA began. Sometimes the penetration will fail to penetrate, though this becomes more apparent when the arrow travels just outside of the hitbox (primarily where bullet magnetism kicks in.) This seems to be an issue with Wish-Ender on its own. I tested Leviathan's Breath, which didn't share the same issue. At the same time, I tested explosive payload weapons, another form of secondary damage, and they didn't have this bug. It's a real pity because I've been using this bow for quite a long time now. This bug is making it rather annoying to use when its exotic overpenetration doesn't overpenetrate.