In my attempts to find a workaround for another issue I am having, I noticed what appears to be a bug with the 'Generate Automatic Supports' function. I have searched the forum and did not find a prior report of it.
When one object is placed on top of another and automatic supports are generated, supports will be created for the upper object as if the lower object was not there. If both objects are to be printed by the same extruder, it's not a real problem because the supports will not be generated by the slicer. If the objects are to be printed by different extruders, it can be a problem.
The behaviour can be replicated as follows:
1. Start a new project and import a 20mm cube.
2. Duplicate the cube and stack one squarely on top of the other using the numeric inputs.
3. Run the dual-extrusion wizard but deselect the option 'Group and align models'.
4. Manually group the two cubes and rotate them 45 degrees on the Z axis.
5. Generate automatic supports with parameters of 4mm and 45 degrees.
6. Examine in the g-code preview.
This is obviously just for demonstration as no supports would actually be needed in the example. The problem came to light when I had a model with areas that did require supports and S3D created hundreds of extra supports unnecessarily. These would have required a lot of work to remove manually one at a time.