RS232 output always follow with an extra 0x0b
Are you sure it's 0x0B? If it was 0x0A or 0x0D that would just mean you're appending a newline/carriage-return somewhere in the MCU's code (I would look at whether the printf you're using does this automatically). 

As it is, 0x0B is the ASCII VT (vertical tab) character. This really smells like something is appending a trailing "end of line"/"end of serial buffer" flag character somewhere.  

Assuming this is reliably and predictably appended at the end of every set of writes to the serial port, you may be able to just treat it as a bonus "end-of-packet" flag for your serial interface. 

Considering the behaviour you are seeing, I would look into how the serial interface is implemented. It's also possible that whatever software you are using to send serial data to the MCU, your serial terminal (or other software) is appending the trailing character.

Have you put a logic analyser or DSO on the serial lines, to confirm the 0x0B is indeed coming from the MCU in the FPGA?

Also, do you have the ability to add standard digital-IO on the MCU? If you do, you could write a small bit-bang serial routine, to localize whether the 0x0b is being appended in the serial receive or serial transmit section of the MCU.



We won't be able to give much more advice without knowing the specifics of your setup.
What toolchain/FPGA soft-core/FPGA-type are you using?