This is by design. AFAIU, an asset can only have a single source. For example, if a PDF file is generated from an INDD file, then the INDD file will become the source of the PDF file. May be you want to relate the assets using "Others" relationship. Can you please explain your use-case a bit? What are these source files (INDD, PDF, etc?) and how are the assets generated from these files?