I'm pretty positive. Yes those are there as hints (very subtle hints) but going from the ashes scene and Huey's departure and then going back to the hospital is a very jarring transition, IMO. There's no proper set up for it.
And again, Code Talker's hint towards Kaz and how Quiet's mission is really just... kind of there. Chapter 2 was meant to be more than just rehashed harder missions and a few new ones.
I'm thinking the Kaz bit, if the game got the chance to resolve whatever Code Talker hinted at, would have definitively transitioned to Mission 46 and been a much better transition.
People would be able to accept the ending better if the game simply had the chance to set it up properly (meaning not just the subtle hints sprinkled throughout Chapter 1) instead of the ending just... happening abruptly in the middle of Venom just declaring they will bring the diamonds of their fallen men into battle or whatever. It's like taking the middle part of MGS2 (like after fighting the Harrier or after Raiden meets the President) and then the ending, where Raiden is fighting off all the Rays, suddenly appears. It's that evident to me there's missing content there to be filled.