Problem: create a square with stroke=0 and fill=100% black. Copy and paste into new document and color swatches are okay. Now go to first document and add a Global Color swatch (i.e. Pantone Green) but don't add it to the square (so it's still stroke=0 / fill=100% black). Copy the square and paste it into a new document. For some reason, that Global Color (Pantone Green) swatch is added to the swatch palette of the new document. Now choose 'Select All Unused', the Pantone Green is selected to prove it's not being used in the element (square) you copy/pasted from the first document.

Add to this: Add another Global Color (Pantone Purple) to the first doc but don't add it to the square. Copy/paste into another new document and only the second color swatch (Pantone Purple) is added to the new document.

Now: Delete the first Global Color (Pantone Green) in the first doc. Copy/paste the square and add it to still another new document. You'll see a color swatch added called 'Deleted Global Color (Pantone Green)'.

I just noticed this bug and posted it in the forums. Another user confirmed they see the same issue dating back several versions. This can be quite a problem when trying to move elements from one document to another.