Well, … there’s a bunch of stuff there that’s kind of a confused mess. There is loose geometry at the Root (top) level that also seems to be a duplication of the same stuff nested inside the wall component.
The window frames are very close, but not quite on the face of the wall. Is that intentional?
FlexTools wall cutters can be great, particularly when you have a zillion windows to cut in like in this example, but I’m not sure I would bother in this case with so few/unique windows.
The window unit and cutting action can all be done in one go if you know how to use it as shown in this example. BTW, the Unlink command just breaks the dynamic aspect of the hole cutting – in a sense it makes the hole permanent as if you had simply created it with native tools.