So I've run into this issue on two separate projects. When syncing with the "Sync Styles" button of the plugin, Craft will sometimes create/add a new, non-exisiting color to the Styles-page. This new color is always 'related' to an actual color used in the document.
For example, one of my colors is #333333, and all of a sudden Craft will create a new color #262626 that doesn't exist anywhere in my designs.
I can select the new color and color pick it to the original, re-sync and it will disappear. But one or more sync actions later and it will randomly reappear. I have this issue for multiple colors. And while it's easy to identify and correct the color above, it's a real horror story when the same thing happens to an array of similar tints that are closely related; it effectively becomes impossible to correctly identify the real color and fix the issue. (Pick the wrong color and you'll send your text styles into a tailspin.)
I've already cleared all my document swatches, so there's no conflict there.
And I'm certain I don't haven't any elements in my document that I've used these colors on. For example: I use #333333 al the time because it's easy to remember and input, but I've never used/typed #262626. And the fact that they randomly return a while later is odd to say the least.
In any case, it's a real drag on my projects and add a lot of work to keeping my styles consistent.