when i have safari open and swipe to the next space, safari appears in the new space. Also when i activate mission control, safari won't show up in any of the spaces. this doesn't happen with any of my other apps.
I think you might have Safari assigned to all Workspaces. If you have Lion, Right click (or Ctrl click) on the Safari Dock icon, Choose "Options" and under "Assign To" choose "None". If you have Snow Leopard, check System Preferences => Expose & Spaces, Under Spaces, check Application Assignment.