Global Color swatch copied into new document even if not used on element being copy/pasted.
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.
The similar problem was resolved recently: https://illustrator.uservoice.com/forums/601447/suggestions/46741123
It turns out the swatch was in use by the plugin.
Can you check all the symbols, graphics styles, anything like this in the document that might use the swatch?
cris black commented
I cannot figure out what is going on with Illustrator (or user error?) ...
If I change a spot color in a design, (ie: Pantone 200 to 202), that unused color will not permanently delete. It goes away for a second and then reappears.
Also, earlier today I did a design and created two of my own "spot" colors to represent a shirt color and white ink. Now every time I open a NEW document, those two colors are added to my swatches pallet and I cannot get rid of them.
While this doesn't seem like a big deal, when it comes to printing films for a spot color job, it runs unnecessary film for each of the spot colors in the swatch pallet. And I just really like the color pallet all cleaned up when I finish a job. That way if it's opened/revised at a later date, the wrong color is not picked. Especially with logo designs where I am sending files to the customer that they will provide to other suppliers.
Running Illustrator 27.0.1
Process Architecture: x86_64
Built-In Memory: 32459 MB