Please stop the PWM and use GPIO to control the output when you need to set the PWM to 0 percent.
Smart answer, But the inverted signal doesn't gave me a waveform that i required during different duty cycles. So for that i badly require a phase shifted one.
For 0 percent, please use the GPIO function.
For other duty cycles, you can still use the PWM function.
It is a known issue for the 0 percent PWM output and our FW engineer are working on it. You can use the above method as a workaround.