Sounds like an oversight to me. Hunts obviously weren't around back the last time this event took place. The way the low level Lightning FATEs work is that there are now two separate copies of the FATE that spawn; one being the one we've normally seen, and one being another one with the same name and description and everything, it just has Lightning appear during the FATE, and apparently the mob is not considered to be the same mob despite having the same name.

If anyone remembers magian trials from FFXI and how they would have you go around killing a specific NM 3-4 times, you'll also remember that even if it was a NM that appeared in Nyzul Isle, killing it there didn't count. You had to kill the "real thing" in its normal habitat.

If they care enough, they might do an emergency maint for it. Since they might not though, about your only consolation is that these FATEs are now considered to be two different FATEs, which increases the frequency that one of the copies will spawn (they just both cannot be up at the same time).o this is sorta similar to that.