The first church started in Jerusalem after Jesus resurrected.
Later, churches were planted in various cities in Israel, Greece, Rome, and other countries.
That's why in the Bible we have letters to different churches. For example, the apostle Paul wrote letters to the Corinthians (church located in the city of Corinth), the Galatians (church located in Galatia), the Ephesians (church located in Ephesus), the Thessalonians (church located in Thessalonica), Romans (church located in Rome), etc.
Today, we have churches beyond these regions.
Over the years, due to some disagreements on theology, we also have churches believing in different things.
However, most theological differences can be reconciled through the Bible. If we go back to the Bible, the Bible tells us exactly what Christians should believe in and what we should do.
But there are some false teachers in the churches and some people who are unwilling to humble themselves before God. This causes division and people doing things that are not according to what Jesus taught.
The Bible predicted that false teachers will arise and people will prefer false doctrines over truth, because the false doctrines sound better to them:
"For the time will come when they will not endure sound doctrine; but wanting to have their ears tickled, they will accumulate for themselves teachers in accordance to their own desires, and will turn away their ears from the truth and will turn aside to myths." (2 Timothy 4:3-4)
These are some reasons why we have different churches.
The first reason is that many churches were planted in different regions but they all believe the Bible.
However, the second reason is that some churches started due to false doctrines and not according to God's word.