This shouldn't happen. Could you measure the VCCD and VDDD pin voltage on board and check if they are normal?
Thank you for your answer
I have checked VDDD and its 3,34V and VCCD is 1,85V
I have set MiniProg3 to supply the Kit at 3,3V and the CY8CKIT-049 is not connected to my PC-USB
I found the problem
I forgot to set the debugging to SWD rather than GPIO
The flag is found in the project under Design Wide Resources - System - Programming\Debugging - Debug Select
Now the MiniProg3 can be used for debugging the CY8CKIT-049-4200