I have a feeling that Danny saw the writing on the wall regarding Kyrie and Anthony Davis pretty clearly at least as early as most of us. But he was somewhat constrained by formality to 'go through the motions'. Danny has talked in the past about how important it is for him to maintain positive relations with all players so no matter what, he was going to go ahead and pretend everything was good and at least extend an offer to Kyrie, letting him be the one to turn it down and go elsewhere.
I think where he got blindsided was in regards to Al Horford. And this seems to have been driven by a handful of factors.
First off: The Durant injury, as others mentioned, opened up everyone to think they could be a title contender. And this made Al a hot property with at least a couple of teams and maybe more willing to offer him 4 year, ~100M packages for the sake of 'win now' moves. I want to make it clear that this jump in Al's price tag was imho almost certainly the biggest surprise factor.
Second: The wooing of Butler away from PHI suddenly opened a slot for a division rival to become one of those suitors.
Third: Al has for years made no secret that he prefers to play PF. Over the first two seasons he was here, he played PF about ~45% of the time. And both his own numbers and the team's performance were measurably better when he was at the PF, as opposed to at the 5. Well, this last year, Al played PF less than 10% of his minutes. I don't know if he ever complained, but I have to wonder if part of Philly's sales pitch was that he would be able to very clearly, right out of the box be starting at PF next to Embiid.