Oh! I think this is an issue related to older saves. I made an overhaul to the Crowd Favor system back in June that caused problems. I had thought I made a retroactive fix, but results have been inconsistent. Can you tell me when you last downloaded the game?
As for Yellow's defeat ending the battle, that is intentional. Blue is coded as a "summon" of sorts.
Can you elaborate on what you mean by "unable to progress" for the Ruruka fight? The clue shouldn't disappear until it succeeds.