If you have some old or wrong mirrors in a mirrorlist then it's currently possible in some circumstances to get problems with pacman 6*, because if you get a 404 message returned it can get mixed up in the download then causes issues. This is currently being patched upstream. Solution: delete corrupted stuff and update / fix mirrorlist.
Or update mirrorlist if it hasn't been done for a while and avoid the issue entirely (although you might not get a problem anyway ;D )