Well, one that comes to mind, which I think even the Apostles had a hard time adapting to, was the change from a religion of a particular people to a religion for everyone. Jesus told the Apostles to go to "all nations" (Matt. 28:19-20), and he is even more explicit on what they are supposed to do in Luke: "repentance and forgiveness of sins will be preached in his name to all nations, beginning at Jerusalem. You are witnesses of these things. I am going to send you what my Father has promised; but stay in the city until you have been clothed with power from on high." (Lk. 24:47-49)
Luke also records this in Acts: "Do not leave Jerusalem, but wait for the gift my Father promised, which you have heard me speak about." (Acts 1:4) To this the Apostles respond with the question: "Lord, are you at this time going to restore the kingdom to Israel?" (Acts 1:6) Jesus obviously wasn't going to reestablish the (literal) Kingdom of Israel at that point, so he tried to show them that the task for them was not to worry about the Kingdom of Israel, but just to go and spread the Gospel: "It is not for you to know the times or dates the Father has set by his own authority. But you will receive power when the Holy Spirit comes on you; and you will be my witnesses in Jerusalem, and in all Judea and Samaria, and to the ends of the earth." (Acts 1:7-8)
The Holy Spirit came (Acts 2:1-4), but they still stayed around Jerusalem for at least a few years. Eventually they did start expanding, not out of missionary zeal, but rather because of persecution: "On that day a great persecution broke out against the church at Jerusalem, and all except the apostles were scattered throughout Judea and Samaria." (Acts 7:54-8:1) And even then they still didn't really get it: "Now those who had been scattered by the persecution in connection with Stephen traveled as far as Phoenicia, Cyprus and Antioch, telling the message only to Jews." (Acts 11:19)
Finally God decided that it was time for something a bit more straightforward, and gave Peter a vision. After this, Peter said: "I now realize how true it is that God does not show favoritism but accepts men from every nation who fear him and do what is right. You know the message God sent to the people of Israel, telling the good news of peace through Jesus Christ, who is Lord of all." (Acts 10:34-36) But because of the activity of Peter that followed this vision, he was criticized by Christians in Judea (Acts 11:1-2), so that he had to go there to explain that Gentiles were now "clean" (Acts 11:4-18).
Unfortunately, as Paul mentions often, many people still didn't get how far reaching the change was (
Wiki has an interesting article on Judaizers). Thus, even some Christians who thought that Gentiles could be saved, also thought that these Gentiles had to follow Jewish practices like circumcision. Eventually Paul had to defend his practices, and the idea that Gentiles did not need to follow Jewish customs, at a Council of "the church and the apostles and elders" (Acts 15), where Paul, Peter, and James together managed to finally give some type of authoritative ruling (though Paul's teachings needed to be clarified again at another Council, as recorded in Acts 21).
Perhaps this is the opposite of what you were after, as you might have been asking about a "bad" or contradictory change. I would say that it was a change that is significant, but not because it makes the Bible look bad, but because it makes the Apostles look a bit... unsure of what to do. Anyway, those are my thoughts (at least for tonight).
Changes in the Bible 
Linear Mode
