There's no evidence that Cookie does much while Safari is open. No sign that it runs a schedule that is set to run every minute. No sign "Remove all Safari Tracking Cookies" and "Remove all Unwanted Safari Data" through the menubar menu do anything. No sign that clicking "Remove All Tracking Cookies" in the Cookie Window does anything.
The Cookie Window says that there are tracking cookies, but no cookies in the list have the tracking cookie icon next to them.
Selecting a cookie in the Cookie Window and clicking on "Remove" does not seem to do anything.
Cookie does seem to remove cookies when I close Safari. And it deletes Safari's history while Safari is open if I ask it to.
Firefox is closed. One Firefox cookie is listed in the Cookie Window. I select it, then click on "Remove". It is not remove. A second Firefox cookie appears in the list. How can that be?
The number of cookies listed next to the browser names and the total of all windows are mostly incorrect.
Is Cookie just not ready for 10.11.1 yet or is there a deeper problem or something that I don't understand?