Same thing here. Got a flag still on a number of areas, one being The Plain, and I'm pretty sure I've found everything there. The level is so small I don't see how there's anything there I could have missed. Guess I'll go through it again.
Edit: Found the one on exterior. You start out outside the Halberd of course. In the first door you go in, when you're inside, you can either go up (with switches for flames) or you can keep going straight right. Keep going right but keep your eye on the ceiling. There should be a part with a crack. I had Lucario, Wolf, and Fox try to break it open, and it did the hit stun effect. I had Toon Link as my last character and threw a bomb up there and it opened up to show a trophy box. Guess only explosives work. May be my problem with the other levels.