Been having this issue, trying to make an instersection with two semicircles and I'm using the mirror modifier to do so. However, when I do that, the best result I get gives me these huge holes. Am I missing something here? How do I fix this so that they are perfectly aligned and do not clip into each other?
Take a cube rotated at a 45 degree angle and use a Boolean Modifier to create a cutout of your tunnel with the perfect shape.
Edit: I just noticed this, in these images my object is actually rotated a bit in Object mode, which is why I have to mirror along the Y and Z axes instead of X and Y