Hi Defonten, I don't think you have any errors in your objects, you're just running into filleting bugs especially for the case of fillets needing to be trimmed against each other.

You might try importing it into a different CAD program which has a more robust fillet engine like ViaCAD or OnShape.

To do it in MoI you'd have a better shot if some faces were combined together, like if this area here was just one face instead of many:



That then simplifies the fillet structure by quite a bit:




The filleter tends to have more problems if you've got small edges, like you've got here due to the segmentation in 2 directions coming close to each other:



I'll PM you back the model that has the larger faces in it so you can test filleting with that.

I made the larger faces by extracting those faces using Edit > Separate, then did an "untrim" (http://moi3d.com/forum/index.php?webtag=MOI&msg=444.4) by selecting all the edges of those faces and hitting delete to remove the trim boundaries and recover the full underlying surfaces, then joined the top edges of those to get back to the original generator curve for those extrusions, then ran the Rebuild command (http://moi3d.com/3.0/docs/moi_command_reference10.htm#rebuild) to fuse those segments together into a single segment curve, then extruded that into the one single face and used Edit > Trim to trim that against the edge curves of the main face followed by Edit > Join.

- Michael