I've experienced this a lot more since and can confirm Koltik's summary. It's a weird bug because in practice it's almost an exploit (having the ability to cleave the cooldown on those important skills can be very strong) but it's actually really annoying because so many of your PVP abilities already use lilies, that having almost everything secretly using them makes you have to think hard before doing anything at all. From the way they've obviously coded it I'm a little concerned that every time we get something new outside of PVP it will end up eating lilies too. I use Bolt a lot and since noticing this I've definitely found the lack of Bolt+Shield or Bolt+boosted Benediction/Assize annoying.