I might as well give my insight.
Aeris's Death: When a player "dies" in combat, it is counted as K.O., which means knockout. So, the player is not actually dead, just unconscious. Thus, using a phoenix down would "revive" them. However, actual death...
Seto Stone: He's probably turned to stone completely from the inside out since he got hit by those arrows, and I'm pretty sure turning completely to stone from the inside out would effectively prevent the use of a soft. Plus, it's been a lot of years since he turned to stone, so using one may not work anymore.
Zack's death: The FF7 group does get hit by a lot of crap, but Zack was gunned down by what looked like an army of Shinra soldiers, as well as helicopters and missiles (I think that's how it played out in Crisis core, it's been a while since i played). Cloud and the gang, i assume, play out their various battles not by standing in one place, but actually moving around, attacking the creatures. Zack was surrounded by an army of guys, having bullets rained down upon him.
Cloud getting stabbed: ... it hit an empty spot...
Shera in the Rocket: uhhh........ Fairies?
There, that's what I got. Tear it apart if you wish, I don't mind. If it don't make sense, I blame my ADHD and lack of ability in explaining crap. The last two parts I didn't give enough of a crap to write anything about, cause it's dinner time.