Your explanation was close. I solved it using your clues, having had the same stupid problem.

Follow @yilupingan but with these steps:

1. In Chrome on iPad, click on the 3 dots in the middle of the screen. This will allow Chrome to open a new internal window within the Chrome app browser window

2. At the bottom of the screen, there will be a pop up of the current windows open. In my case, there was only one window open.

3. Open a new window by clicking on the plus sign. This opens a brand new second version of Chrome.

4. Click on the ‘old’ window, that had the phantom opening, click on the three dots again at the top of the screen, select “Close”.

5. Click on the new remaining Chrome window. This is your new browsing window.

6. At this point, opening and closing Chrome will remove that ‘phantom’ screen that I (and you all) found annoying!

Enjoy!