Apple - Random Untitled Folders Appearing
Ok so I finally figured out the issue (at least for me). It turns out that some games when you have multiple monitors do not use true full screen and so right clicking can create accidental new folders to appear on the desktop.
In particular the game League of Legends was culprit in this. I found out after doing some more research and noticing this only seemed to occur after the game. There does not appear to be a remedy for this yet.