You can split the body into two, do the cut extrude and then combine back (see attached part). Added a video in case you can't open the file.
For 3d printing issue, please check the settings on the machine OR talk to guy running the 3d printer as the wall should be solid.
Massive thanks Deepak, Not only a solution but a video to explain it.Awesome..
For completeness, I spoke to the 3d printer guy, he says the problem is that the thickness of the walls is not a multiple of the printers minimum bead. ie two beads side by side is not thick enough and 3 is too thick so it tried to "space it out" with a gap. He didn't seem to think there were many printer settings in the package we have.
So I have changed the thickness on this one adn we'll see how we go