Just how did they recover the statues covered with Coco's doodles, anyway?
Why does IBF stay intact for 17 years, while the entirety of LeMU is rebuilt around it, and while it still draws power from the same source as the rebuilt LeMU? One would think Lebleich would try to destroy IBF to cover up the evidence that they were behind the creation and outbreak of Tief Blau.
Sara mentions that the Frozen Tuna might have washed out of the kitchen's fridge. If there was a kitchen, why were the gang stuck eating sandwiches to the point where they got sick of them? And what about the first incident?
The food got ruined by the sea water and they had difficulty cutting up the tuna. For the second incident, they had to recreate the events in order to trick BW, even if it means getting tired of chicken sandwiches.
In Remember11, it's established that Leiblich Medizin has owned a functioning time machine since at least July 2011. With that in mind, and with the knowledge that they used it for such mundane purposes as saving an executive's ex-girlfriend, how was the 2017 incident ever allowed to occur?
The mechanics aren't perfect. They would have to account for distance and barometric pressure. I don't think they'd be able to build a replica of Lemu in secret.
Why is that Kaburaki could sleep so well in the Pressurization Chamber? That's because he was already more than used to situations like this one. It's been 17 years, he's probably gone through extensive training for this very day. It wouldn't be a stretch to think that training has made him accustomed to sleeping in this kind of enviroment.
Why are the Life Readings shown fluctuating between 5, 6 and 7 people in Kid's route? It took me playing Virtue's Last Reward before I personally got it, but... Remember how Schrödingers Cat goes? The cat in the box is neither alive, nor dead. We cannot know which until we open the box - well, who else do we also know who is stuck in a 'box' with no certain way to affirm they're dead or alive? Yup. Takeshi and Coco. Now, how many people were trapped in LeMU? Not counting in Sora, who doesn't have a body and thus can't register in the Bio Scan, there are 5 people. These 5 people plus the 2 not-dead-nor-alive people in IBF makes 7. Since the fate of Takeshi and Coco are uncertain, the number flickers between 5 and 7 depending on the state the two 'cats' are in! This can double as Fridge Horror, since this essentially means that every time the numbers '5' and '6' are shown, it implies that either one or both of them didn't make it.
We could also apply Shroedinger's Cat to the elevator scene as well. Before opening the door, you hear both Coco and Sara's voices when only one of them are actually present. You don't know which route you took until you open the box.