This one's kind of awkward.
Windows 8.1 RTM
MMix64 1.11
1) Open a Metro app as a desktop window. Make sure it's focused. I discovered this issue while I had the Music app focused.
2) Pull down from the top edge of the screen like you'd normally do to close a fullscreen Metro app or the Desktop.
3) Windows will behave as though the Metro app you had focused was fullscreen instead, so it will be like you're trying to drag-down for that app instead of the Desktop.
To keep that Metro app as a desktop window, you must now drag to the left edge and stick it back into the side tray. Otherwise your only other options are to either put the app in fullscreen/snap mode or close it.
If you choose to drag the app back to the left edge panel, the desktop will reappear, but clicking anywhere on it will open the Start screen.
I don't generally ever need to drag-down-close the Desktop on my PCs, but I occasionally trigger the action accidentally, and it's pretty jarring when this happens.
Otherwise just a minor weirdness.