jcroslan picked out some interesting log lines that indicated the hardlinking step was failing. After ruling out incorrect API usage, I thought the layer was broken until I realized there's a corner case in layer application: because layers are defined to be applied to a filesystem in order, it's perfectly valid to create a hardlink in a higher layer if it's known the file will be present from a lower layer.

So this should get fixed to redirect all dangling hard links to an empty file. NB it can't be a file like /dev/null because hardlinks cannot span a filesystem, and /tmp is usually a ramdisk.