the reason why the new faces keep appearing is because the window isn't connected to the outer edge/box. all vertex's need to be connecting to something. Booleans are abit of a pain when you work with cyclinders with lots of vertices.



the reason why that wierd line is happening is because there are extra vertices which are not needed and creating stretch in your mesh. you may need to move some vertex's as they will be hiding underneath each other



hope this helps abit