This is simple to reproduce, and happens only on a retina display.
Open ST: http://prntscr.com/gl435j
Go to fullscreen (CMD+CTRL+F): http://prntscr.com/gl439u notice the grey bar at the bottom.
Exit fullscreen: http://prntscr.com/gl43ea notice how the three buttons (top left) are a little bit on top of the Folders in the sidebar, and the tabs are now at the very top of the window.
If you open more tabs, some of them will be behind the window title: http://prntscr.com/gl43iz
This only happens with ST's new adaptative theme, and on a retina display on macOS.
With a non-retina monitor (1080p for example), entering and exiting fullscreen works fine. No glitch.
That's it, i guess.
In another unrelated topic: kudos for the ST3 release. Gladly paid for it as soon as i saw the good news.