I have spent 30 minutes typing up a bug report and it won't submit. I will post my situation here.
Today is just after the update for the Leviathan event to go live soon. I suspect this may be the reason.
Mirror matches with Piett ship, Executor. My opponent's ships get permanent target lock and breach. Call in Slave 1, but seismic blast is on a 3 turn cool down.
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"the first time all enemies are breached while Slave 1 is active, or if Slave 1 enters the battle while all enemies are breached, Seismic charge's cooldown is reset"
I've noticed that when you hit contract it applies undispellable target lock and breach to the enemy ships (like normal). But whenever the enemy calls a reinforcement, it does not apply the undispellable breach anymore, only the target lock. So I'm assuming your enemy called in slave 1, it did not apply the undispellable breach, and then you called in your slave 1 afterwards, which would mean that his cooldowns wouldn't reset because all enemies aren't breached.
Edit: FWIW, someone else made an Answers report: https://answers.ea.com/t5/Bug-Reports/Executor-not-applying-breach-properly/m-p/12758699#M66706
This is from the update notes for yesterday’s update. I don’t have Exec yet myself but hope this helps clarify something to someone.