Since the thread got bumped, I'll post this now:
1) Nameless Hill is broken.
Basically, if a tile is one space from you and has a flower/patch of grass on it, you can walk there. Even if it's supposed to be a cliff:
[attachimg=1]
(there's a flower under Rumia)
By using this, you can skip pretty much the whole thing, up to and including Medicine. I've included a map with the faulty collision spots in the attachments.
Muenzuka is also broken in the same way. (it's more minor, but skipping most random encounters by taking the scenic route through the grass field above is still not really good)
2) Reaver is broken.
First,
2499 crit damage. That's ridiculous by early game standards (Reimu goes down in 3 criticals. Sariel - in about 4.).
Now, it
might have been fine if the crit chance was sufficiently low. Unfortunately, that's broken too. (for reference, Reaver's current chance to crit is
~100%)
Here's a showcase of Reaver's brokenness. Even some superbosses don't fare that well.3) The scene upon entering the Garden of the Sun after getting Wriggle is bugged, as it throws you back to the original map even if you're in the endgame.
4) Everything Nitori gives you for glass shards becomes unobtainable when you start the endgame. Also applies to Patchoulli's Magic Amplifier.
5) If you enter the Namazu battle with Wriggle dead and then somehow finish it with only Tenshi alive, you get a Game Over.