By dock do you mean the Swatches panel? Have you tried the Delete Unused Panel Items action from the Action panel. They can also be in Symbols or Brushes but if you run the action it will delete them in order so that the color swatches are deleted last and if they were in a Symbol, Graphic Stlye or Brush with the original gone they should delete. Also make sure that everything is visible and unlocked.
As well as what Larry says, select and delete stray points. These may carry spot colours, styles etc.