Thanks for the replies. I think my confusion re the cutter was that the video showed the cube detaching from them when grabbing and moving whereas mine stuck to the cube. I guess the parenting is why and the outliner change just added to the confusion whether I’d messed up.
I did make progress with the holes not showing. I think it was related to the cutter edge meeting the cube overlapping with another. The cutter area was fine to overlap but not the connecting edge. I resized the cutter slightly to avoid and got holes for all.
