Disagreements among God's people have existed from the days of the first apostles. One reason for this is that our minds are imperfect and warped by sin. So our understanding of God and His ways is imperfect. Paul says, "We see through a glass dimly" (1 Cor.13:12). So, when we try to understand God's will in different situations, our perceptions can be different. We must all be humble enough to acknowledge this, at all times. But this does not mean that we have to live in ignorance of God's ways forever. As we wholeheartedly seek to obey God and thus grow to maturity, our understanding of the will of God will become more and more perfect.
So immaturity among leaders is one reason for disagreements and divisions. When Paul and Barnabas were young apostles, they separated from each other, after having worked together as a God-appointed team, because they disagreed on whether to accept a younger coworker (Acts 15:36-40). They were immature then and did not know how to resolve their dispute. But God still had mercy on them and continued to use them.
At times, however, divisions occur among God's people, because self-seeking, dominant brothers seek to build their own private kingdoms in the church. The Ephesian church split into many factions after Paul left, because self-seeking elders drew away little groups after them (Acts 20:30). Demas, Paul's coworker, left him, because he sought after something in this world - perhaps money, or the honour of men, or a personal following (2 Tim.4:10). The same thing happens today as well.
Two areas where there can be major differences of opinion among Christian workers are money matters and church-leadership matters
The way we acquire money for God's work is a very important matter, because Jesus said that God and Money were the only two masters in the world (Lk.16:13). Money for God's work must be acquired the same way that Jesus and Paul acquired it: They trusted their heavenly Father and told Him alone about their monetary needs.
We too should never make our monetary needs known to human beings, because we have a rich heavenly Father. A billionaire's son would be insulting his father if he were to ask anyone else for money. In the same way, we insult God when we make the monetary needs of our ministry known to men. This was why Jesus and the apostles never revealed their monetary needs to anyone. They only told their Father in heaven - and He provided all their needs in abundance.
In church-leadership matters also, we must follow the pattern taught in the New Testament exactly: Church-leaders must build their churches as a body where each member is encouraged to fulfil his function - and not as a congregation, led by one man. They must constantly train younger men and lead them to maturity so that those younger men can gradually take over the leadership, as soon as possible. Paul urged Timothy to train younger men who could train other younger men (2 Tim.2:2). This is the new-covenant way of ministry. But sadly, just as King Saul was reluctant to vacate his throne in favour of God's anointed, David (1 Sam.18:8), there are many "Saul's in Christendom today also who are reluctant to give up their thrones to younger men. Such elders are a hindrance to God's work, however gifted and good they may be in other ways.
Jesus and the apostles have given us the right pattern to follow in both the above areas - and that is what everyone of us must follow, if we are to build new covenant churches.
We can certainly fellowship with ALL born-again believers - even with those who disagree with us in the above matters - provided they have a pure heart (See 2 Tim.2:22). The Bible warns us however: "Keep your eye on those who cause divisions and hindrances contrary to the teaching which you learned, and turn away from them. For such men are slaves, not of our Lord Christ but of their own appetites; and by their smooth and flattering speech they deceive the hearts of the unsuspecting" (Rom.16:17, 18). So we must totally avoid fellowship with believers who cause strife, who promote divisions in the church, who have a spirit of accusation, and who pollute our minds in any way.
And when it comes to working together, we can do so only with those who have identical views with us on the important matters we have mentioned here. "Can two walk together unless they are agreed?" (Amos 3:3 - KJV).
Many disagreements are minor and we can overlook them and work together with brothers who disagree. But the matters mentioned above are major.
We cannot make even the smallest compromise when it comes to such major principles taught in God's Word. If, as a result of our taking such an uncompromising stand, some brothers leave us, then we must let them leave. We should not hold them back, at the price of compromise. Each one must choose for himself whether he wants to go the way of total obedience to God's Word or the way of compromise in such important matters.