If you have Gap Check on and are seeing the connection you can turn it off by unchecking Gap Check in the menu > View > Gap Check.
Also, if we adjust the 'Maximum Gap' slider in the Fill Tool options menu (over on the right) that will adjust the sensitivity of Gap Check.**
**Note: Adjusting Maximum Gap can cause some issue with backward compatibility in Opentoonz release prior to the introduction of the Maximum Gap slider.
I'm investigating what you have stated concerning the two shapes and the false reporting of gaps. If you can supply a sample project that displays the problem that will help tremendously.