I get accurate results when measuring capacitors with my NanoVNA so I assume it is something with your setup or calibration. Without photos or screenshots we don't have much to work with here.
Here is a measurement of a ceramic cap marked 485 pF that I made with a NanoVNA. I compared it to a measurement made with a DE-5000 LCR meter at 100 kHz. The estimate of Rs is poor under 500 kHz when the reactance is very high. But capacitance measurement is quite good.
Roger Need
