Thank you very much for the kind words! I'm really glad you're noticing the comments, believe me they get me stuck sometimes, haha!
About the targeting, that's a common RPG Maker glitch unfortunately, it happens when your mouse cursor is hovering over a target. So your mouse cursor was probably over the boss during the fight. Always keep the cursor away when in battles. That should fix it!
Grace's special move removes Protect status from enemies. There's a chance for the boss to cast Protect on itself, if that happens you'll do little to do damage to it. Then you'll have two options: wait for the status to go away by itself. Or use her skill to break his protection!