Only a little of that green liquid spilled out after Rufus shot the box. Kadaj was distraught and though that the contents had been damaged beyond use, but clearly he was wrong. It's the same box later, with the same slightly-mangled head of Jenova's corpse, sans a few drops of blood.
Seriously, people will try to find a "plot hole" in anything in this film; it's like they're on a desperate quest to further justify their dislike of it.