I believe this issue has been resolved in the MacOS High Sierra upgrade, but you can give these steps a try:
1.
Open Safari
2.
Clear existing cookies by clicking ‘clear history’ from the Safari menu in the top left corner of the screen
3.
Quit Safari
4.
Open Finder
5.
Click the ‘Go’ menu —> ‘Go to Folder’ OR use the keyboard shortcut ⌘+⇧+G
6.
Copy and paste this exact phrase into the box:
~/Library/Safari/Databases.
7.
Delete everything inside of that folder
8.
Again, click the ‘Go’ menu —> ‘Go to Folder’ OR use the keyboard shortcut ⌘+⇧+G
9.
Copy and paste this exact phrase into the box:
~/Library/Safari/LocalStorage
10.
Delete everything inside of that folder
11.
Open Safari
12.
Check to see if the issue is resolved
I believe this issue has been resolved in the MacOS High Sierra upgrade, but you can give these steps a try:
1.
Open Safari
2.
Clear existing cookies by clicking ‘clear history’ from the Safari menu in the top left corner of the screen
3.
Quit Safari
4.
Open Finder
5.
Click the ‘Go’ menu —> ‘Go to Folder’ OR use the keyboard shortcut ⌘+⇧+G
6.
Copy and paste this exact phrase into the box:
~/Library/Safari/Databases.
7.
Delete everything inside of that folder
8.
Again, click the ‘Go’ menu —> ‘Go to Folder’ OR use the keyboard shortcut ⌘+⇧+G
9.
Copy and paste this exact phrase into the box:
~/Library/Safari/LocalStorage
10.
Delete everything inside of that folder
11.
Open Safari
12.
Check to see if the issue is resolved
Try going to Safari/Preferences/Search and unchecking Include Safari Suggestions and Show Favorites.
As per this article See your Top Sites - Apple Support
You can quickly see the websites you visited recently and most often on the Top Sites page.
You can also see the Top Sites page when you open new tabs. If you don’t see the Top Sites page in new tabs, change settings in General preferences.
Remove a Top Site: Hold your pointer over the Top Site, then click the Remove icon  that appears. You can also drag the Top Site away from the window, then let it go when you see the Remove icon , or Control-click the Top Site, then choose Delete from the shortcut menu.
It seems all you need do is delete your history. I don't even want that to happen, as I want my Top SItes to remain where they are. However, if I delete the history (no cookies, or anything else) , most of the Top SItes vanish right along with it! What's the point of clicking the Pin option, if they don't stay stuck?
What are you attempting? Try not using Safari but other browser apps. Or just use Safari in private mode.
How to delete frequently visited websites
