The only time I've seen apocalypse go off was in a wild pet battle. I had killed the cockroach and missed my trap on the 2nd pet way too many times so this match lasted to the 15th round. When apocalypse went off, it "missed" both pets, a humanoid and a critter, and we just kept on fighting.
Marcellus wrote:One thing I know about apocalypse is that it will miss if your roach is dead before the meteorite landing.
There are several abilities that are bugged in this manner; most secondary effects cease to function if the pet that generated them is defeated, or sometimes even just switched out. It really restricts strategic setups.