Does not need to be "the same" time, and is not the same time
Notice that the Mk 15:25 (3rd hour) is stated as "when they crucified him." In the Jn 19:14 passage (6th hour) the reference is to when Pilate sat in his place of judgement for the final condemnation of Christ to the cross.
There are time differences
The easy way to state it is that there are at least two main time reckoning systems that are being referenced. Commentators vary in that some will call one set the "Jewish" reckoning, and the other the "Roman," and others will refer to them in the opposite fashion. For purposes here, all that matters is the fact that the two differing systems existed. I will also refer to one set as "Jewish" and the other "Roman" based off what the majority of commentators I have looked at tend to equate the periods with, and that this Jewish reference supports.
So in parallel with our modern clock times, we have the following (note that this is an approximation for the Jewish reckoning especially, as they actually divided the daylight hours into 12 [cf. Jn 11:9], which may be more/less than a true hour depending upon time of year, etc.):
12 mid - Roman start of day | Jewish 6th hour night
3:00am - Roman 3rd hour | Jewish 9th hour of night
6:00am - Roman 6th hour | Jewish start of day (sunrise)
9:00am - Roman 9th hour | Jewish 3rd hour day
12 noon - Roman 12th hour | Jewish 6th hour day
3:00pm - Roman 3rd hour | Jewish 9th hour day
6:00pm - Roman 6th hour | Jewish 12th hour (sunset)
9:00pm - Roman 9th hour | Jewish 3rd hour of night
It is well attested that Roman's reckoned the day from midnight.
What is debated is whether they reckoned the hours of the day from that point or not.1 There seems to be evidence that both forms of reckoning were used, which is really enough to open the possibility that the two schedules resolve the issues between the gospels.
About the Situation Eliciting this Question
A Possible Time Frame Given the Evidence (times are approximate)
5:00-5:30am Early in the morning (i.e. the dawn's morning twilight; Mt 27:1; Mk 15:1; Lk 22:66),2 the Sanhedrin had already gathered for the "quick" trial of Christ at this time, and then sent him to Pilate while it was still "early" (Jn 18:28).
5:30am-6:30am Examination of Pilate, then Herod, and Pilate's delivering to scourge Jesus, and his final judgment to crucify him (Herod must have been nearby, his palace was not far from where the action was, but he may not have even been there, but rather nearby in the judgment area itself).
Map from http://www.ccel.org/bible/phillips/CP051GOSPELMAPS.htm
Note that John only says "about the sixth hour" which leaves a fair bit of play for actual time (perhaps even up to 7:00am). This would be Roman reckoning if the time frames are going to fit,3 which also fits the audience John would have been writing to, being after the destruction of Jerusalem in A.D. 70.
9:00am About this time, the 3rd hour by Jewish reckoning, that Jesus is actually nailed to the cross (Mk 15:25), the final mocking of the soldiers and march to Golgotha being the span of time between.
12:00 noon - 3:00pm From the 6th to 9th hour (Jewish reckoning), darkness comes "over all the land" (Mt 27:45; Mk 15:33; Lk 23:44). At the end of this time is when Christ actually dies (MT 27:50; Mk 15:37; Lk 23:46; Jn 19:30).
No Day Discrepancy
Some have noted that there is not only a supposed time discrepancy, but also a whole day discrepancy. Jn 19:14 states "it was the Preparation Day of the Passover" that Christ is before Pilate and dies later that day. This is deemed to be in conflict with the synoptic gospels that note the first day of the feast of Unleavened Bread, when the Passover is to be killed (i.e. the day that Jews are preparing to observe the Passover), was the day before the evening meal with the disciples in the upper room, and so they had prepared the passover during that day (Mt 26:17, Mk 14:12, Lk 22:7). Thus the supposed day discrepancy.
However, the Synoptic Gospels themselves speak of another preparation day, which does align with the day Christ is crucified. Matthew 27:62-64 (NKJV for all quotes):
On the next day, which followed the Day of Preparation, the chief
priests and Pharisees gathered together to Pilate, saying, “Sir, we
remember, while He was still alive, how that deceiver said, ‘After
three days I will rise.’ Therefore command that the tomb be made
secure until the third day, lest His disciples come by night and steal
Him away, and say to the people, ‘He has risen from the dead.’ So the
last deception will be worse than the first.
Recall that Joseph had rapidly buried Jesus right at the end of the day of crucifixion, during the evening twilight hours (Mt 27:57) before the setting of the sun. At sunset would have been the start of the Passover itself, and it is that "next day" when the chief priests make the request above. That is, they requested this of Pilate after sunset, right after Christ was buried in the tomb by Joseph.
Mark 15:42 states:
Now when evening had come, because it was the Preparation Day, that
is, the day before the Sabbath, Joseph of Arimathea, a prominent council member, who was himself waiting for the kingdom of God, coming and taking courage, went in to Pilate and asked for the body of Jesus.
This puts Jesus being crucified on a day of preparation. As also Luke 23:50-54, which states:
Now behold, there was a man named Joseph, a council member, a good
and just man. He had not consented to their decision and deed. He
was from Arimathea, a city of the Jews, who himself was also waiting
for the kingdom of God. This man went to Pilate and asked for the
body of Jesus. Then he took it down, wrapped it in linen, and laid
it in a tomb that was hewn out of the rock, where no one had ever lain
before. That day was the Preparation, and the Sabbath drew near.
So John's statement "it was the Preparation Day of the Passover" (Jn 19:14) is not referring to the preparation day for the Passover, but a special instance of a preparation day for the Sabbath that was following the day of the Passover, and thus the preparation on the Passover day for the next day's Sabbath. That the priests had not yet eaten the passover the morning Christ was crucified (Jn 18:28) was because they had been busy about handling the matter of capturing and condemning Christ that night, before the first day (daylight hours) of the feast. They still wanted to partake, and thus did not enter the Gentile domain of Pilate in order to not be defiled before they could eat (which was all very hypocritical of them).
So all four gospel accounts have it on a day of preparation for the Sabbath day that was following the Passover day that Christ was crucified.
1 D. R. W. Wood and I. Howard Marshall in New Bible Dictionary (Leicester, England; Downers Grove, IL: InterVarsity Press, 1996) argue Roman and Jewish accounting of hours in a day matched. For one who considers the time schedule reversed between Jewish/Roman reckoning, see Norman L. Geisler, "'Avoid… Contradictions' (1 Timothy 6:20): A Reply To John Dahms," Journal of the Evangelical Theological Society 22 (1979), 64 n.17, where he refers to the works of the 1st century Jew Flavius Josephus' biographical work "The Life of Falvius Josephus." However, in my looking up Geisler's reference, it appeared to me that the 6th hour by Josephus' reckoning was in accord with the Jewish timekeeping I've given above.
2 Using information from the twilight page, a "rough" calculation for the Jerusalem area would put the twilight time before sunrise at 28-39 minutes.
3 I do not hold to a hermeneutic that allows for John to change the time/day for "theological purposes." I hold that the Bible is God's word, absolute truth, and inerrant in what was originally recorded and within what has been preserved for us from that original in the copies (note that this does not mean each copy is inerrant, only those that are truly copies that match the original reading, which we have within the extant manuscript copies we possess today).