Hi Thorin, please post the .3dm file with your square and cylinder in it as a file attachment.
You might have some kind of arrangement where the pieces are barely grazing each other. If the result would have an area of zero "wall thickness" like it has an inner and outer wall that are pinched together that could be an invalid self-intersecting volume.
It's not really possible to diagnose what might be going on from just a written description though, please post the .3dm model file so I can examine the geometry.
Thanks, - Michael
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