I know this game is pretty dead, but just in case anybody comes along (like I did). On the mission "The Brand's Guidance". If you go too fast through the 3rd part (after opening the first two gates) the boxes will be glitched and you'll have to wait a sec for them to be destructible. I'm not sure how fast is too fast, and if it's even a 100% guaranteed glitch. I've had this happen using the hawk of light feather on zodd, which can reach pretty insane speeds.