Best glitch was Abysmal Labyrinth's boss spawn while at the 10 floor confirmation dialogue.
For those who suck, the Abysmal Labyrinth is a boss rush of sorts. You fight up to 50 bosses in succession to get labyrinth seals, to get awesome unique weapons. Every 10 floors, you can opt to escape and keep your hard earned seals, or risk the next 10 floors for a chance to get a lot more seals. However, if a boss spawns while you're confirming whether you should go on or not and he kills all your party members, you don't get shit!
I had Coelacanth spawn in such a situation. It was very unpleasant.