Yes, you are right. just took another -6 cards for failing with their Vault, and it isn't mentioned in any public threads.
If I understand it correctly, Team Water used more of a certain card than they had in their vault. If they used 15 cards and only had 13 in their vault, a 6-card penalty isn't enough. Whichever deck was listed last in the deck listing thread was illegal and should therefore have been disqualified.
I'm pretty confident SG is being lenient because it was accidental and this should have been caught when decks were submitted, at which point Team Water should have been penalized and made to modify their submission.
As is, if I were Team Entropy or Team Aether I'd wonder if I was beaten with an illegal deck. I don't harbor any ill will against Team Water. But using cards not in the vault should be looked at as a serious violation in the future.