At the moment msys2-20180531 is installed, which contains a pacman binary too old to read .zst archives, which are how newer packages are being compressed. This means that it's very easy to run pacman -Sy and get into a broken state, because pacman can't read the archive necessary to upgrade pacman. The only way out of this is to either install heaps of packages with -U or just nuke the msys directory and start again.