The Thunder Ball quest requires you to "Successfully perform Weather Cloud Tempo 3 times", but no matter what I try, I can't get my Weather Cloud Tempos to count towards the quest.
I am finding a similar issue with the Tempo Training quest, where it does not count my progress towards "Perform 3 unique Tempos".
Lastly, the Sorcery Clima Tact quest has what might not be a bug, but maybe an oversight? The reward for the quest is the Sorcery Clima Tact, but requires you to "Kill 10 enemies using Thunderlance Tempo", and I have only been able to use Thunderlance Tempo with the Sorcery Clima Tact in hand. I have been made aware that the Sorcery Clima Tact can be purchased from traders and so it's still completable in Survival, which is why I'm not certain that this one is a bug.
Edit: Thunderbolt Tempo and Thunderstorm Tempo don't seem to attack enemies when used with a Weather Egg.