Can you check in the System tab of .cydwr i.e. the design wide resources file, if these pins are selected as GPIO or SWD in the Debug select option?
You need to chose the pin function as GPIO, this will allow routing signals to these pins. In this case, you will still be able to program the device through these pins but not use these pins for debugging.
One more question.
Can I use Pin 11 and 12 for UART (Tx Rx) routing in same IC CY8C3866LTI-068?