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Save the asembly as a part then save that as an STL. You save an assembly as a part by doing a "Save As"
When working with the assembly, you could also click "Save As" and change the file type to STL. Once this is selected, click "Options" and under file format click "STL." Then there will be a check box that says "Save all components of an assembly in a single file." Click this box, click ok, and click save. Everything should work fine then.