PCB Dielectric Coefficient for FR4 is not constant by frequency so that the manufacturers give this coeffcient for certain frequency,temperature and relative humidity.Therefore the dielectric coeffcient which you used to calculate characteristic impedance for PCB traces migh not be correct.
In additional to, if the operating fequency is sufficiently high, this coefficient may vary very much with frequency that's why you traces can have a different impedance.
Finally, manufacturing tolerances may be high and this impact- especially at very high frequencies- trace caharacteristic impedance.
Rigid cables are more reliable and trustable compare to PCB traces.