Question #684770 on Yade changed:
https://answers.launchpad.net/yade/+question/684770

Robert Caulk proposed the following answer:
Hello,

During the polyhedron intersection check, it finds a determinant = 0
[1]. My guess is that you have a flat tetrahedron or something similar
leading to two rows or columns of that particular system being
equivalent. Of course, an MWE is necessary to know exactly what is
happening.

Cheers,

Robert

[1] https://gitlab.com/yade-
dev/trunk/blob/master/pkg/dem/Polyhedra_support.cpp#L371

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