Ok turns out there was a secret hole in my cube under the roof so i couldn't see it.

so i managed to get one window sorted. then i copied the polygon i used, and select the face on the bottom and extruded it to make the window taller.

Then when i try to do the same boolean difference (on the same polygon) i get the window but also some odd black artifacts around it (like someone literally punched a whole in the wall).

what causes these?

I've attached a pic of it.