Port order mismatch from spectre simulation

I have a case where adding the extracted netlist causes spectre to return port order mismatch.
I have compared the port order in both netlists (extracted and pre-layout) and they match perfectly.
I simulated with the extracted netlist ONLY and it completes successfully.
Similarly, with ONLY the pre-layout netlist, it completes successfully.
But combining the extracted and the pre-layout netlist causes port order mismatch error.
I will appreciate if you can provide any suggestion or clue as to the cause of this error.