Basically, it doesn't happen if you transition from phase to phase (take the previous phase to 0% yourself and then transition to the next), but if you commit damage in a phase, after it has already been completed by the guild, then when you enter the next phase the boss starts with cooldowns at 0 (at least P1-2 and P3-4). I hope that makes it more clear.
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This has been flagged as a bug and sent up to our team for review. Thanks!
@Zabak while Team CG is looking into this, see my thread here for more information and to help you and your guildies:
https://forums.galaxy-of-heroes.starwars.ea.com/discussion/84424/bug-tank-phase-bosses-can-start-on-0-cooldown
Basically, it doesn't happen if you transition from phase to phase (take the previous phase to 0% yourself and then transition to the next), but if you commit damage in a phase, after it has already been completed by the guild, then when you enter the next phase the boss starts with cooldowns at 0 (at least P1-2 and P3-4). I hope that makes it more clear.