That happened to me when removed a grade. I lost 75 points. I don't understand why it happened, but when I removed my C grade in something (It was one of the original things the type had that I had no intention of using anytime soon), and I turned off everything else as well except for one type, which was 100+400, so I should have been at 500 used, but I removed the C and I was still at 575 used. NOTHING else had a single grade in it, just one weapon type at B.
Note: I don't think that it's permanent. It seems to reset when you change types, and possibly reset the game. I've since switched to a different type, but this made me go back and check it out. I have my points back, not exactly sure when it happened, but I know at the time it annoyed the hell out of me because I couldn't get a grade in a weapon I wanted when I should have had the type points. Since, though, I've switched to a different type, and I went back to look to see if it's still there and it's not, it's reset itself. Your Extend Points probably reset themselves when you switch types, so when you switch back it fixes itself.
I've also encountered the Awoken Serpent issue myself while playing on Infrastructure Online. I've never gotten this issue in Local Online.
I've also seen an issue, probably not a bug, possibly intentional, where Nanoblasted Beasts cannot enter Boss waiting zones. So if you accidentally turn on your Nanoblast 2 feet from the door, you have to wait for the entire thing to end before your party can enter the boss.
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