Can't rearrange Mission Control spaces
Just to reconfirm that I understand it correct, the issue is: 

On trying to move full-screen apps between two spaces by going into spaces (press F3 button or 3-finger swipe above), it (full-screen app) just slips to one the desktops and doesn't get accommodated like desktops (space is created automatically by the GUI for insertion and you can drop the desktop there). 

Have found the following: 


Generally restarting the Mac solves this issue for some time (few days) but then it returns again. 
Once the full screen app drops into one of the desktops, pick it and insert it where you want in the top spaces panel. 


This is not exactly a solution but a workaround or change of habit if you don't want to restart your mac for something so trivial.

Hope this helps in reducing the inconvenience.