- Why is Shin suddenly beatable in your third encounter? During his first appearance, he can't be damaged and you're required to stall him until the 'Out of time...!!!' message appears. Ditto for the second fight, except this time you're meant to lose via Total Party Kill to advance the story. Then when you fight him the third time in Eluria Tower, he can be hurt (and slain) despite the characters having never gained any Applied Phlebotinum weapons or 11-Hour Superpowers in the interim.
- Why doesn't Ronyx/Ronixis order his crew to warp out of their current position before the Calnus is destroyed? Sure, the sudden attack is unexpected, but his crew are able to detect the beams before they hit AND quantify the level of power in each one. You would think evasive maneuvers might be their #1 priority after surviving the second shot, knowing they can't take a third.
Headscratchers / Star Ocean: The Second Story