macOS Sierra 10.12.5 (and prior):
When am using and viewing an app in full screen mode
(such as, but not limited to,
and the program opens a new window,
the window will open in the virtual desktop intended for full screen use,
rather than on an adjacent virtual desktop intended for desktop use.
The main problem with this is that if I do not move the new window, then when the full screen window is selected and comes to the foreground, it will completely eclipse the new window, which will become unselectable without using alternative means (alt+tab, etc.)
It should not be the intent of full screen viewing to open other windows on the same screen as the full screen application.
For clarification: in
virtual desktops intended for desktop use are labelled "desktop X",
where X is an integer number, (such as 1, 2, 3, etc.)
Virtual desktops intended for full screen use of a specific app are labelled
with the name of the app.
Chrome and other internet browsers make poor examples,
since these generally work as intended.
Note: Even if I request a new window within the app and immediately switch to a virtual desktop intended for desktop use, Mission Control will switch back to the full screen window and open the new window in front of the full screen app.