Not sure if this is a bug but it is something that I experienced while playing. After ignoring Tycho's advice about going to the Periphery I finished the game to get the fake ending. Having saved before doing so I figured I could access any save after watching the credits. When selecting continue the only save I could access was the top save file. I was able to resolve the issue by quitting out of the game and then launching the game again. Not sure if anyone else has experienced.