If you want to get technical I think that the in game interpretation is that a Phoenix Down is only usable on enemies that are mortally wounded but not dead yet. Aries probably passed that threshold while they were fighting JENOVA.

But even then I don't really think factoring Phoenix Downs into the scenario is necessary. I could understand the confusion if Phoenix Downs ever appeared as part of the story, but I think it is obvious that they were just in battle items to enhance gameplay.