Although the Jews began their days at dusk and Romans began their days at midnight, that is not how either civilisation measured the passage of time. Simply speaking, the mechanical clock had not yet been invented. E. G. Richards describes in Mapping Time how shadow clocks were used to divide the hours of daylight up into exactly 12 hours of variable length according to the season. Measuring time accurately at night was also possible, based on the stars, but difficult and of no interest to most people. It was not until the invention of mechanical clocks that we changed over to a variable number of hours of daylight, each of fixed length throughout the year.
Using the universal shadow clock, the third hour was the third of daylight and the sixth hour was precisely noon. Thus, they were never the same hour. The explanation is that we find not one but two differences between Mark (and the other synoptic gospels) and John, not only in the time at which Jesus was crucified, either the third hour (9 o'clock) or the sixth hour 12 o'clock), but even the day. Mark says that the Last Supper, on the evening before the crucifixion, was also the Passover feast. John 19:14 tells us that the crucifixion took place on the day of preparation for the Passover. Ian Wilson says in Jesus: The Evidence it is possible that John, in his desire to represent Jesus as the new “paschal lamb”, distorted history to have the crucifixion occur when lambs would have been slaughtered in the Temple in preparation for the Passover
For theological reasons, the author of John has changed both the date and time of the crucifixion, to coincide with the time that Jews killed the sacrificial lamb for the Passover. In John's Gospel, Jesus is, by analogy, the lamb of God.