In regard to the various death penalties under Jewish law, not counting crucifixion (as the film claims the Jews ordered), hanging the corpse on a tree until sunset is part of the death penalty. Since the Jews had no authority to execute anyone while under Roman occupation, having the Romans crucify someone they regard as a blasphemer was the next best thing to being able to carry out the penalty themselves.
While it might not be all that comforting to contemplate, when you read the original account in The Bible, does it ever occur to you to wonder why Jesus was quite dead by the end of the day? Roman crucifixion victims sometimes took days to die since none of their major organs were damaged and the entire method was intended to maximize the victim's pain and suffering. This dramatization visually spells it out for you: more than a few who underwent the kind of scourging Jesus did never made it to the cross. After taking so much punishment, it's arguably a small miracle that Jesus lasted as long as he did!
And normally crucifixion victims weren't flogged precisely because it would kill them too quickly. Note that the other two crucified with Jesus are mostly unwounded.
As Jesus predicted, Peter denies knowing him three times. Earlier, Jesus asked Peter if he loved him, three times, as a counterbalance.
Which is pretty much how the Bible work. According to the Gospel, when Christ rised, he once again asked Peter thrice whether he loves him. Each time Peter answer in affirmative, Jesus instruct him what he should do.
When Jesus made a table with a higher height, Mary expresses amazement at the height of the table he's making. Jesus explains that it was ordered by a wealthy man. Mary asks if the man likes to eat standing up. Jesus chuckles and explains the man wants to use "tall chairs". Mary laughs and says... "This will never catch on." Of course he knows it's gonna catch on: not only does he have omniscience, it had been said eating from the sitting position is tied to the rise of Christianity - and being the son of God, he has lots of wealth in heaven - he's dictating how we should eat!
Jesus seems to suffer a dose of Overdrawn at the Blood Bank... but when a faithful go to a Catholic/Orthodox/Anglican Mass, said faithful realized that it is not wine or "Jesus Juice", but had transubstantiated into the actual blood of Christ. Then the faithful suddenly realize that Gibson had actually placed one of the core dogma all over the flim, in that the Mass is exactly the same sacrifice of his passion, and the blood of Christ is truly presented.
Meta example: When this movie was being made, a lot of people thought Mel Gibson was being artsy and pretentious, with the resulting movie being regarded as anything from Torture Porn to a deep religious experience. Then came Gibson's anti-Semetic rant. Consider this: Regardless of one's personal beliefs, Jesus was a deeply influential Jew who started a major religious movement. That means that Gibson got to show an influential Jew being tortured horribly over the course of three days movie-time and three hours real time and call it art.