I don't think this was only a bad day.
He had enough chances to test the legs, even on Sunday he could stick it in more in the "why not, eh?" way, so my thinking was the he is either waiting for a nuclear snipe when he decides to do it, or that he just doesn't have it. Not only was it not nuclear, it was being happy to lose only the time that was lost.
So I'm inclined to think, he just doesn't have it.
As to why, probably only him and the team know.
Maybe the hope was that by pacing they would prevent attacks from others, but for that Kuss would have to go to the front after Denis, or just pace it a bit slower through the whole day, so the team would last a bit longer with the pacing. Of course this strategy makes sense only if you think others are stronger.
Since they went harder than they could, they maybe didn't expect this outcome either, but I'm not sure if that's because they expected Roglič to be better, or others to be worse. In the first scenario, there is maybe still a glimmer of hope, in the latter, well, gg.