I can't begin to count the number of times Reprisal has saved a party from wiping, even in dungeons. When you use it and the party survives with 1% health you know that you saved them. Just use it before an aoe cast ends.

It's intentional because some boss casts spawn other entities. If the entity is somewhere else (you can see if an entity spawns in the enemy list), then just use it on something else. You can use area mitigation such as Troubadour, Tactician, Shield Samba, Divine Veil, Passage of Arms, Shake It Off, Dark Missionary, Heart Of Light or any healer mitigation.

At least in old fights, it's not intended to herd the group to use them on different enemies, because not everyone used to have it in the past at least without leveling other jobs to cross-class with.