System Information
Operating system: Linux-5.13.0-7614-generic-x86_64-with-glibc2.33 64 Bits
Graphics card: Mesa Intel(R) Iris(R) Plus Graphics (ICL GT2) Intel 4.6 (Core Profile) Mesa 21.2.1

Blender Version
Broken: version: 3.0.0 Alpha, branch: master, commit date: 2021-10-14 17:43, hash: rB89c7c115cebb
Worked: Error was introduced in https://developer.blender.org/D12862

Short description of error
In geometry nodes, the behavior of the Mesh Boolean node is unpredictable and arbitrarily returns either no geometry or incorrect geometry (i.e. geometry that has not had the boolean operation applied to it).

Exact steps for others to reproduce the error
Open the attached blend file before and after D12862, or:

• Open blender and create a new Geometry Nodes on the default cube
• Remove the default link and create a cube mesh primitive
• Add a transform node to that cube primitive with a suitable scale like [0.5, 0.5, 2] or something else that should create a proper intersection
• [optionally] Add a Realize Instances node
• Add a mesh boolean node, set the mode to difference, plug the realized original mesh primitive cube into the first input and the transformed mesh primitive cube into the second input, plug the boolean node into the final geometry output