Why did splits take place in the early Church if it was moved by the Holy Spirit?
The question could be phrased: Were splits already present in the New Testament and how did Jesus handle these splits?
See this link to a lot of biblical verses that show other people preaching in the Name of Christ, but their preaching is not one with the Apostles during Jesus' time on earth.
When Others Preach
Interestingly, Jesus did not prevent the people from preaching in His name, even though it's obvious that they are not one with the Apostles;
Mark 9:39-40 ESV
But Jesus said, “Do not stop him, for no one who does a mighty work in my name will be able soon afterward to speak evil of me. For the one who is not against us is for us.
So, it is evident that there were splits, but Jesus also knew that the Church or the faithful Christian will benefit from this split in ways known only to God in His mysterious Wisdom. But of course, the desire of the Eternal Father was given to Jesus, and the established Church founded by Jesus Christ will fulfill the desire of the Father for all the People of God who are preaching in the name of Christ to unite together as one. Maybe not unity in the expression of faith but unity in the expression of love. After all, the gospel of Christ teaches that the greatest of all this in not faith but love.
Jesus Prays for All Believers
20 “My prayer is not for them alone. I pray also for those who will believe in me through their message, 21 that all of them may be one, Father, just as you are in me and I am in you. May they also be in us so that the world may believe that you have sent me. 22 I have given them the glory that you gave me, that they may be one as we are one— 23 I in them and you in me—so that they may be brought to complete unity. Then the world will know that you sent me and have loved them even as you have loved me. (John17:20-23)
Pope Francis has a better way of answering your question with this statement;
Freedom is a right of every person: each individual enjoys the freedom of belief, thought, expression and action. The pluralism and the diversity of religions, colour, sex, race and language are willed by God in His wisdom, through which He created human beings. This divine wisdom is the source from which the right to freedom of belief and the freedom to be different derives. Therefore, the fact that people are forced to adhere to a certain religion or culture must be rejected, as too the imposition of a cultural way of life that others do not accept;
Justice based on mercy is the path to follow in order to achieve a dignified life to which every human being has a right;
Dialogue, understanding and the widespread promotion of a culture of tolerance, acceptance of others and of living together peacefully would contribute significantly to reducing many economic, social, political and environmental problems that weigh so heavily on a large part of humanity;
Dialogue among believers means coming together in the vast space of spiritual, human and shared social values and, from here, transmitting the highest moral virtues that religions aim for. It also means avoiding unproductive discussions;
The protection of places of worship – synagogues, churches and mosques – is a duty guaranteed by religions, human values, laws and international agreements. Every attempt to attack places of worship or threaten them by violent assaults, bombings or destruction, is a deviation from the teachings of religions as well as a clear violation of international law;
In closing, it is true that the People of God have different expression of faith,culture, etc. but we only have One God and One Maker. The One Omnipotent and Omniscient God who made all of us has a Divine Plan written in His Divine Wisdom and no angels and man combined can stop the Will of God. So, in the end as Jesus prayed to all believers and reminded us that the Will of the Father is to unite all his children as one in the unity of love. The question is, will this happen? The answer is YES!.
Isaiah 55:11 King James Version (KJV)
11 So shall my word be that goeth forth out of my mouth: it shall not return unto me void, but it shall accomplish that which I please, and it shall prosper in the thing whereto I sent it.
So, the Will of the Father is to unite all the People of God and Jesus already prayed for all believers and the Church Mission as inspired in the Vatican II Teachings is to unite all the People of God by preaching & witnessing the Infinite Mercy of God.
The People of God will be united by the Holy Spirit by pouring in abundance the "merciful love of the Eternal Father", the Father is Rich in Mercy as St.John Paul II encyclicals teaches. The Infinite Mercy won by Jesus Christ at the Foot of the Cross, and the Church Mission written in the Bull of Indiction of Pope Francis titled Vultus Misericordiae is the key to unity.
BULL OF INDICTION
OF THE EXTRAORDINARY
JUBILEE OF MERCY
BISHOP OF ROME
SERVANT OF THE SERVANTS OF GOD
TO ALL WHO READ THIS LETTER
GRACE, MERCY, AND PEACE
Pope Francis beautifully said this words to remind all the People of God that now is the time to unite and implore all the Pastors to wear the "cloak of compassion and mercy" and go after the lost and wounded souls in all the four corners of the world.
"The Divine Mercy is Infinite but the Time of Mercy is Not." (Pope Francis)