Fridge Logic - At the beginning of the game, you have to get an item called the Star Crest. While several characters talk about how important it is, it is never spoken of again after obtaining it.
That One Boss - Garados. He use ice attacks, he can avoid your physical attacks and he can confuse you. The fact that you can only fight him with your main team while only having two characters doesn't help either.
Booth, second follower of Homncruse, is widely agreed on to be one of the toughest fights in the game, having very powerful magic such as Bomb Lv 2.