Become a MacRumors Supporter for $50/year with no ads, ability to filter front page stories, and private forums.
So good news - looks like this functionality has been fixed by the kind folks at google.

I can verify this, as I just downloaded Chrome on my iPhone and search history items delete as expected when you individually delete them.

OP, you could have also deleted these by tapping the three horizontal dots at the bottom right, then tap on Settings > Privacy > Clear Browsing Data

 
Register on MacRumors! This sidebar will go away, and you'll see fewer ads.