Ensure there are no conflicting SWCs in your build path.
Run the patch tool from the command line to get verbose output: patch listing error flex 3
# For SAP JSPM
./jspm.sh -verbose
Inside SAP JSPM, the EPS/incoming folder or the SDA (Software Deployment Archives) may have partial downloads. The flex_3 parser cannot read an XML patch listing that is cut off or has invalid characters. Ensure there are no conflicting SWCs in your build path