Whoa, thanks a lot for the in-depth testing! I'll try and get them fixed for the next update, this helps a lot!
I'll have to look into what's causing all of them, I know 1) has always been a huge issue, with freezes with some grapplers making their enemies get stuck in their target state, I'll try to make it match Mugen for the next update. Flickering is an interesting observation, I can imagine a few things causing that, will probably have to go through that frame-by-frame to figure out where it's getting the bad state info from. 2) is interesting, might be some trigger failing related to the on fire sprite effect? But yeah, I'll have to take a deeper look. 3) might just be that flag check missing like you wrote. I don't remember there being an invulnerability check based on the ground flag, so this is probably a bona fide oversight.
So yeah, thanks a lot again for the in-depth debugging and info, really super helpful, and thanks a lot for taking the time to share it with me!