In 4.1.1 there no longer is a close button in the upper right corner of the Transmogrify-window when using the ElvUI Skin, it's still clickable if you press in the right spot:

Should be fixed in the next update

So the button re-appeared again randomly at the same time the ElvUI integration broke again as per my comment here: #256 (comment)

As per my comment #256 (comment) the close button only seems to work when the skin breaks upon initially loading into the game. After a /reload the skin works again but the close button disappears.

this issue also happens with any menus opened using betterwardrobe, mainly the details cageing list and item sources list.