Could you attached your test project?
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I attached the new project which can measure the duty cycle of PWM signal.
You need to check the PWM capture and reload trigger signal. And the getcapture API parameters.
capture2 = Cy_TCPWM_Counter_GetCapture(Counter_2_HW, Counter_2_CNT_NUM);
capture = Cy_TCPWM_Counter_GetCapture(Counter_1_HW, Counter_1_CNT_NUM);