Auto updater fails (0.13.1 -> 0.13.2 right now) when it tries to overwrite (or remove?) file which doesn't exist.
In my case it's factorio.pdb. I keep my whole game folder on SVN so it's synced between PCs

Message is "Error when opening Q:\...\..\x64/factorio.pdb for reading: No such file or directory". It might be similar for other files.