OP is assuming many facts.
Let’s take an example, the Council of Jerusalem, all of the Christians there had disagreements on many issues concerning practices and ritual, having to do with Judaism. All of the Christians in there were of the same Church, they were no divided just because they thought you should circumsize , or because you shouldn’t. No they were not 2 churches, they just had disagreement. What they did? Paul came and through prayer , all leaders and elders of the church that were apparently not of the same exact thinking, got to an agreement to what they thought " It seemed good to the Holy Spirit and to us " . That church was at will to discuss this matters, that church was very humble. They discussed the issue in a respectable matter, they didn’t closed up their minds and said “No I am right because I have the lineage back to Jesus”. No, they discussed it and declared the new teaching. But of course nowadays no one is willing to discuss this matters and other matters, because everyone is right. Paul and Barnabas hold that is not essential to circumsize but some of the others thought it was essential. After debate and discussion the whole church agreed with Paul’s argument and agreed with it. So they made it official.
JL: The Church with the Holy Spirit still uses councils to settle matters of dispute. You will notice the council made the decision and all accepted that descission. The matter was settled in the whold church.
ACTS 15, FIRST COUNCIL OF THE CHURCH
The apostles and elders gathered to consider the matter, should Gentiles be circumcised Acts 15:6, After much debate,
Peter rose and told how God chose him, that from his mouth the Gentiles should hear the word and believe, and said why put a yoke on disciples which neither our fathers nor we have been able to bear? Acts 15:7-10. Then he gave the defining teaching,--
we believe we shall be saved through the grace of the Lord Jesus, just as they (Gentiles) were, Acts 15:11. After Peter had spoken the assembly kept silence, the debate was over and settled, Acts 15:12.
Then the assembly listened to Paul and Barnabas relate the signs and wonders God did through them among the Gentiles, Acts 15:12. After Paul and Barnabas spoke, James replied, "Symeon has related how God first visited the Gentiles to take out of them a people for his name. And with this the words of the prophets
agree, as it is written, I will rebuild the dwelling of David which has fallen, Acts 15:13-21,
that the rest of men may seek the Lord,
all the Gentiles called by my name, Acts 15:17, (in other words, a regenerated spiritual Universal (Catholic) Davidic Kingdom and the King, the Son of David, Jesus, will build a new Temple (his body the church) for all nations, for God his Father. Christ appointed ministers and gave the keys to the kingdom to the chief minister St Peter. Go teach all nations=universal=catholic, baptizing them in the name of the Father and of the Son and of the Holy Ghost, Mt 28:19).
James did not make the decision but gave evidence from scripture, for Peter’s definitive teaching. James goes on and says, Simon has
declared. Therefore my judgment (opinion) is, and James goes on to proposes a pastoral compromise of rules or laws for discipline in churches where there is a mixed Jewish and Gentile fellowship, to prevent divisions or offense, This seems good to the
Holy Spirit and to us, Acts 15:28.(apostles and elders in assembly=council Acts 15:25). Those in Antioch when they heard the letter rejoiced at the exhortation, Acts 15:30-31. Why, because it came from the Apostolic Fellowship and therefore they knew it came from God.
Notice how this division in Antioch came about; We have heard some persons
from us (Apostolic Fellowship) have troubled you, although
we gave them no instructions, Act 15:24. These men, not sent by the church, went out on their own authority from the fellowship, teaching, apart from the Church, as doctrine their personal interpretation of the scripture. They caused confusion in Antioch. To settle the dispute they sent Paul and others to go up to the Apostolic Fellowship (take it to the Church) in Jerusalem to settle the doctrinal dispute.