One thing about web apps that I have noticed - Say for example I open the CNN web app, view some content, then close it by clicking on the “X” in the top right corner, then I open the New York Times web app. I now have two Chrome tabs open, one with CNN, and one with the New York Times. Closing and clicking on a third web app gives me a window with THREE tabs, etc.
The only way to avoid this behavior is to close the TAB instead of closing Chrome altogether.