Hello,
I just took one use case which might not be applicable to your case, but explains situation when high frequency PWM may be a limitation in terms of ADC sensing. If you are sensing during the pulse, then it's probably ok.
Anyway (and in any case), have you tried to make a snapshot of your signal along with the PTU trigger signal? PTU can generate trigger signals in debug mode and the signal can be evaluated in terms of ringing. The current signal should be measured at the output of the opamp, BEMF voltages on the phases, DC bus voltage on the HD pin => I still suspect the ADC signal is not sampled correctly.
If the signal is ok, it might be loss of commutation (e.g. due to interrupt overflow, which can be partially solved by assigning higher priority to the commutation event).
Another reason might be the overcurrent comparator - even if the average current is within limits, there still can be some ringing on the signal, which might trigger the overcurrent event and based on the action, it might disable the motor. It would be indicated by the GDUF flags.
And for example, if the low-side MOSFETs are not switched on for sufficient amount of time, based on the bootstrap circuitry design, the bootstrap capacitors might not be fully charged, which may lead to the high side MOSFETs to lose one or more switches (it highly depends on the hardware desing - if you have your own, it is probably designed correctly, but for the development kit / EVB, I would be careful about the operation at high PWM frequencies).
Please let me know how the investigation goes.
Regards,
Matej