I get:

"Copying clonedcontainer crate_01_de_melothes00000002. Save game may contain invalid data.

Continue running executable?"

Everytime I load the game. How to fix this? I have no mods installed.

EDIT: Nevermind, it went away on it's own.

This error pops up very rarely, so I don't think anyone really found out what causes it, and it doesn't seem to have any bad affects.
But saving, exiting, reloading should remove the warning.

It's always best to keep a few back-up saves, just in case.