Jeff Johnson via Michael Tsai:

DuckDuckGo still uses JavaScript to intercept your link clicks, and there’s no good reason for it. One consequence of this clickjacking is that your Safari browsing history gets messed up.

This explains why some sites are missing in Safari history. Also, when I type in the search bar and then open a suggested link that was discovered via a DuckDuckGo search it brings me back to the search results instead of the site.