In my experience the Google tool is just not smart enough to figure out clever CSS or other techniques you may have used to make your screen mobile-friendly. For example, I have had tables which remove columns depending on the screen width and even used bootstraps "table-responsive", but until I put in a pointless div to style "overflow-x:auto;" it reckoned the content is wider than the screen. Similarly, I drop some clickable elements on a small form factor but Google still reckons clickable elements are too close together even though they don't show on a mobile device.
It's just a dumb tool, you have to find workarounds or dumb down your content.