Why aren't nasdaq.com and yahoo.com removed when I clear Safari website data?
Those are likely &quot;perma cookies&quot; which are cookies that use javascript and other methods to make the cookies persistent even when you have explicitly removed all cookies. Which is annoying as hell and a known issue.
I found an Apple discussions post that purports to show you how to delete these.
Which boils down to

So the path is:
~/Library/Safari/Databases/__IndexedDB/

Just delete the folder of the cookie you no longer want