Oh, so I think this is a combination of several things.
Thing the first: because I am silly, the game doesn't mind if you have two savegames which have the same name. You can save as many games as you like with the name "Listic" and it just won't care. I should really fix this because it gets confusing.
Thing the second: if you played the previous version of the game and left some old saves lying around, the game automatically updates them to the new save file format.
So those two things together mean that if you had a bunch of old saves lying around with a name that you've also been using for new saves, the game will just update those saves and make them available to load.
Needless to say I'm at the VERY least going to make it impossible to save a game using an existing save name.