All Desktops swiping brings the app front When an app is selected as all desktops while switching from one desktop to another even though another app is in front of this app, it automaticly brings the app front then puts it to behind again. To prevent this I always have to hide the app before changing desktops. Is there a general setting which will prevent this?



While swiping left to right from behind of xcode to front of chrome then goes behind of chrome.
As long as another app that is set to None or This Desktop in the Desktop you are swiping from is the Active Window, and you did not make the app set for All Desktops active during the session on the previous desktop, then the Window that tracks to the All Desktops will remain in the background without coming forward and then going back. 

This behavior only happens when the All Desktops App is the Active Window when you swipe to the new desktop. I assume the reason for it is that the OS X designers felt that swiping and hiding the open windows on the new Desktop could cause confusion, so they added this animation to emphasize that the Active App from the previous desktop is deprioritized and that there are open Apps on the new Desktop.