We can speculate all we want, and we will only find out when the race is over, if ever.
If it's a bad day after a rest day, if it's Bernal's back or if he's fading.
I don't think it's the later, 2 days ago he put 45 secs on the next rider in Giau. And today he only conceded against Yates (and Caruso 3"), but did better than the rest.
I better think this is a different Yates (not his brother, though). The one who we only saw a bit in Zoncolan. The fact that S. Yates also had a minicrisis in the last Km shows he was going full gas.
As
@roundabout said: Bernal was probably overconfident following Yates, and didn't dial down when he was in the red.
I guess he should have responded to Yates, but Bernal's mistake as he called, was to dig too deep into red. He should have assessed earlier and tempo'ed with Martínez. I guess he would have lost less time, and probably finished ahead of Caruso