Alright, so I went through and tested every character's: jab, tilts, pummel, throws, smashes, aerials, grounded specials, aerial specials, and landings on aerial moves. Also tested Peach, Link, Y.Link item throws. I found a few more things:
Ganon:
Neutral B cause a freeze when started on the ground, but works normally when started in the air, even if landed during the animation.
Link:
Aerial down-B into aerial forward Z-throw causes a freeze, even if there is a landing between the Aerial down-B and throw. No problem with grounded down-b into grounded forward Z-throw, aerial down-b into grounded forward Z-throw, grounded down-B into forward aerial Z-throw, or any c-stick throws.
Mewtwo: down-b works (both aerial & grounded), but neutral b causes a freeze after a short time (both aerial & grounded) without sound effect starting
Marth: being hit (activating) down-b (both grounded & aerial) causes freeze. If not hit, no freeze.
Roy: being hit (activating) down-b (both grounded & aerial) causes freeze. If not hit, no freeze.
Repeated from before:
Ganon: u-tilt causes freeze
Jigglypuff: landing during b-air causes freeze, inputting f-air causes freeze
Edit: Also, the grounded endlag on Roy's neutral B seems crazy long.