Because the rules are stooopid! (I laugh, but it's true).
Well, under 6.0, from what I understand from people who responded to me in from the stupid questions thread, Zayak was mandatory -1. Which gave the judges more flexibility to respond to different scenarios, since people rarely got 6.0 technical merit. Browning won Worlds over Petrenko despite Zayaking, because he did more than Petrenko. Kulik lost Worlds to Eldridge by Zayaking, since he did less than Eldridge (one less combo, iirc). So at least in terms of zayaking, 6.0 was less stooopid.
Fernandez should have done a 3Toe at the end of his program! That always should have been his training plan if he tripled out on one of the Quad Sals. Yes, though, the rule is stupidly implemented in CoP.
However, I still probably don't feel he should have finished above Ten or Takahashi if he had gotten more credit for the 3Sal at the end. It wasn't a great performance and his SP was a mess; he was overscored in that segment and should have been placed 8th in the SP.