In iOS 9 Safari keeps track of your frequently visited sites. These sites are displayed alongside your Favorites when you open a new tab. You can disable this feature by following these instructions:
1. Open your Settings app.
2. Tap on the Safari panel.
3. Tap the "Frequently Visited Sites" slider so it is OFF / WHITE.
Now the Frequently Visited section will not be shown when you open a new tab.
To delete an individual frequently visited site just tap and hold the site thumbnail until the Delete option appears.
You can learn how to clear your entire Safari browsing history here.