Unfortunately, it's a known bug. It's actually like that for the 360 as well. But on the 360 if you have more then 1 Manual save it will only overwrite the original, so you might want to try that if anything.
On that note, I'd like to see the non bulk patch downloads they were talking about to fix some of this stuff. I mean it been almost two weeks since the game was released.
I know. I stated that if you have more then 1 manual save it only overwrites 1 of them. I have multiple characters and every time I started a new one it would save over 1 of my other manual saves, but it didn't matter since I keep a few just for that purpose.
Probably because I have Auto-save on still.
I've never had it override a manual save. It makes sense that it'll override the Auto, as that's gonna be based on the character you are currently playing as. People just need to pay attention to what they are doing.
It's overwritten my manual save twice. That's enough for me. It's happened to other people as well.