Why do my apps open in a single space when resuming? When I restart yosemite and I select 'reopen windows when loggin back in' I have a lot of apps that open in the same space.

For example when I have sublime text and libreoffice open in a space and restart, the space they they were on will be empty. They will all be on a single space but only in the mission control view and not in the actual space.

In contrast to safari and other osx native apps. I would just like to be able to shut down my macbook and resume in the exact same way. Is there a setting for the apps to resume in the space there were on, fully openened?
Not certain in Yosemite, but in Mavericks apps would only restore to the Space they were on if they were set to specifically open in a given Space - otherwise they would all huddle together on the front-most Space at launch.

Right click the app in the dock to set to 'This Desktop' once you have it in the correct one.

Quickly move an app to another Space by left-click-hold the top bar of any window then hitting your key-combo for the desired Space.