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I have a simple model with two pipes as below
I then try to join the two pipes with a horizontal pipe via an axis as below. I select extents to be "To" and
select the right vertical pipe. The extrusion works and mates with the pipe.
I then extude to the other pipe and I get
It cuts through the body of the reference pipes. I have the model here in the gallery
https://fusion360.autodesk.com/projects/extrusion-bug-example