Maze-level map, five mazes which are then linked together and filled out with rooms. This devlog series didn't get a third installment yet because I was lazy and my unlaziness was put towards the game itself, but it'll give some clarity on the process: https://www.youtube.com/playlist?list=PLvccjxfjJs1StJsQBnYxw-gp32J80Q4mO
I don't know for sure if that's what happened here, but to be clear, what you describe does match a known issue. Based on playing and completing seed #649 now on desktop, but right after loading the game, I think this was some shenanigans I've seen happening on successive generations after a single play, where sometimes the game will fail to generate the proper items on subsequent plays. Obviously nobody wants the generator to punish players for playing more, so that's going to be a thing to hunt down for the next release. (Regarding fresh generations, there is still a small danger in my mind and probably by the numbers of those going haywire, and there are some plans to quash that danger as well.)
(BTW, if you're interested in taking on beta testing capacity officially for the Super version, once I have builds that hopefully fix some of these more egregious generator issues, you can find me as kkairos@gmail.com or as 'kaikairos' on Discord.)
Thanks again for testing and reporting!