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Making unions, intersections and such

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Hello,
this is the question regarding the "Internal error in geometry decomposition" message that I'm consistently getting. What I'm trying to build is a 3D RVE of particulate composite (see attached picture). Each sphere has a soft shell and a hard core. So the shells can overlap, cores cannot. Also shells of course cannot penetrate the cores. I generate random 3D seed with spheres of prescribed size distribution (Gaussian in this case) using my own C++ code. Then input everything into COMSOL, sphere by sphere. By playing with Compose boolean operation I managed to remove parts of the shells that were protruding into cores (see one of the steps attached). Now I want to unite the shells. Two (in red) got merged without a problem. When I'm trying to add the third one (the bottom one) I get the geometry decomposition error. This error appears persistantly for a range of tolerances from 1e-03 to 1e-10. This is where I hit the wall really. What causes this error? Is there a better way to make such geometry? Tweaking repair tolerance helps in some cases, but does not in many cases. What do I do then (tolerance is the only variable I can change in this process)? In fact, quite often application of union results in dissapearance of the objects I was truing to merge. I guess I just don't get this logic.
Any help is much appreciated!
Thanks!

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