Hi @giraffe508 thanks for the reply.
This is how I downloaded the BSDL file (see attached picture) and I doubled checked again.
So there is a possibility that there might be something weird with the jtag debugger I am using a FT2232H controller for the boundary scan. The Jtag debugger jlink ultra+ give a ID of attached image.
Converted ID to binary:
ID: 01011011101000000000010001110111
CPUID: 01000001000011111100001001110010
From what I can see the ID reported form the jlink ultra+ and the FT2232H is the same. As you mentioned it is not critical error but for how we aim to use the JTAG live test software is to give the MCU module we created to someone with not necessarily all the knowledge of how they work to be able to test the module so this might cause problems in the future.