[gotham]

I don't think it's a scaling issue, as the 'service module' section builds, but not the 'command module' section. If it was a scaling issue on printing, I would assume to see problems with all parts, not just some. As I mentioned, the diameters of the parts don't seem to match.
As an alternative build I tried your Apollo Command and Service module, but the diameter of the service module does not match the diameter of the base of the command module cone.