In general, gedit opens new files in the same window adding a new tab to the workspace. To open a file in a separate instance or window of gedit is easy.
Once you have a file opened as a new tab, just right click the tab containg the file which you wanted to be opened in new window and select “move to new window”. It should open file in new window.
Alternately, you can use gedit –new-window command in console to open a new instance of gedit.