At Stu's request, here's how to drill a hole in a pipe.
From left to right:
The pipe with the "drill" in front of it. The drill is just a cylinder of the desired diameter placed at the desired angle.
The pipe with the "drill" moved into it. Note the lack of a line along the intersection of the pipe and the drill. These parts aren't really intersecting yet.
Select the "drill", right click and choose Intersect with model.
Delete the "drill". Note the cursor pointing at the blue edge. This is a back face, the inside face of the "drill".
Select the outside surface of the pipe, right click and choose Orient faces.
Will that work for you?