I have never had that problem on Windows 7, I do not remember if I had experienced it with windows 10. I suspect it is like any software, some play nice on some systems but not everyone's.
The problem is that Microsoft with their UWP apps threw out the rule book of how to detect applications that are running and what it means for an application to be closed (UWP apps are never really closed, they remain suspended once you open them for the first time). Also, since UWP apps are not Win32 applications, they don't even have an embedded icon (but rather a combination of separate PNG images) - the combination of these factors results in the blank entries you see on dock applications not updated to be fully compatible with Windows 10.