@Dr_Professor83 I won't tell you the solution for the third mystery, I'm interested to see if you'll be able to solve it without an impending deadline.
But the culprits for the second mystery were Krauss, Natsuhi and Jessica. Eva and Nanjo said that everyone who was confirmed dead was actually dead - if you look over when the adults found their children, they all said some variation of "my child dead". All except Natsuhi, who said "Jessica...how could this happen". Then when it came to the final part, Natsuhi just said that they were there, not that they were still dead. Lastly, Erika said they used tape etc to close the room in the same fashion as other rooms, but she didn't say the room was sealed or that it was as effective. Natsuhi tried to pass it off as such, though. And also, when Krauss was finding the master keys, he usually referred to people as corpses, but with that room, he just said he got it from Maria and Jessica, without actually confirming their deaths.