Glad I could be of help!
Yeah, I forgot about the little boxes next to the day and room name, should have suspected that to be meant as a way to tell the time.
The scenes that are marked as completed before watching them are only the ones that trigger automatically. Since they still trigger anyway it isn't really a gamebreaking bug, just harder to track which scenes have already been seen.
Glad I don't have to do the "Explore Boundaries" mission to see everything. At least the narrator (you :p) agrees with me on these scenes.
Regarding the Supply run & Gacha, I'm playing on PC. I don't know, if I'm even supposed to be able to click on resupply. When I close the Gacha screen without clicking on it, I can't reopen it. Which might be another bug, I honestly am not sure if I have more than 1 supply or not.