The app.activeDocument.swatches.getSelected() method gets an array of selected colors in the Swatches panel of the document. What happens when you apply colors from the array to selected objects? If you select one path in the document and apply a color to it, all swatches remain selected.
If many paths are selected, applying a swatch to any path resets the color selection. If you create a script to paint objects with selected colors, it makes the user’s job more difficult. To run the script again, the user has to select the swatches again.
My bug report on Adobe Illustrator Uservoice.
