I am an Independent Baptist, but I am not above saying that there may be heretical teachings in my denomination that I was unaware of until now. I'm kind of wondering what they are.
This is a good, humble attitude to have. Basically what you're asking is to understand Church history. That's a lot of ground to cover, too much to do it justice through forum posts, but I can try to help.
To start, how do we know anything about what the early Christians believed? We have the Bible, yes, but how did it come to us? Ultimately it came to us through preservation by Christians over the centuries (and Jews, in the case of the Masoretic Text, but that's getting into the weeds a little too much).
What came as a surprise to me when I first started looking into all of this was that the Bible wasn't the only thing these early Christians preserved. They also wrote theological works that were preserved. So for example, we can know what the early Christians believed about baptism and communion, about how we can distinguish between legitimate and illegitimate spiritual authorities, and many other things.
We know from history that the church was always organized; Paul writes about the qualifications for becoming a bishop and the process of ordination involving a laying on of hands from those who are themselves already ordained. Clement of Rome in the 1st century and Irenaeus of Lyons in the 2nd century attest to the continuation of this process and its importance as a means of identifying legitimate spiritual authority: if someone was a bishop in this line, or ordained as a priest under a bishop in this line, and held the true faith, his authority was legitimate.
There were times when people would begin teaching new doctrines, arguing that their new doctrine was the authentic Christian teaching. These controversies were usually addressed by councils after the model of the Council of Jerusalem in Acts 15. The biggest councils were called ecumenical councils - ecumenical meaning "worldwide" or "empire-wide." The first two of these gave us the form of the Nicene Creed we have today and condemned heretics who said that Jesus Christ wasn't God and that the Holy Spirit wasn't God.
When these councils condemned heretics, the heretics didn't immediately give up and say, "oh well, guess we were wrong, we repent." Some of them probably did, but for the most part they just separated themselves from the Church and retreated to an isolated geographical area. Arianism, for example, which taught that Jesus wasn't God, stuck around in the European barbarian tribes for a few centuries. These separations are called "schisms," and are spoken of in 1 Cor. 12:25. To clarify, schism was more often than not a small, local issue, and most schisms died out fairly quickly because there was a common understanding that legitimate authority necessarily required ordination from other legitimate authorities.
The first schisms that have lasted until today were the result of the third and fourth ecumenical councils. These were over differences in teaching about the nature of Christ. It's from these that the modern Assyrian Church of the East and Oriental Orthodox come, and these only recognize the ecumenical councils up to the ones they disagree with. In their view, they continue to uphold the authentic Christian teachings and those who accepted the councils were wrong.
The next lasting schism came in roughly the 11th century as the Roman Catholics and (Eastern) Orthodox went into schism over a variety of issues, mostly relating to doctrinal and disciplinary changes Rome had introduced. These each still consider themselves the Church (with a capital C), the legitimate continuation of the spiritual authority that started with our Lord's commission given to the Apostles.
Denominations come in in roughly the 16th century. There had been a kind of perfect storm brewing in western Europe for the past few centuries: a few proto-protestant groups had arisen, there was growing dissatisfaction with abuses within Catholicism, the printing press had been invented and allowed fast distribution of written works, and the German princes were itching for a way to redirect money that was being sent to Rome into their own treasuries. So when Martin Luther began teaching Lutheranism, instead of fizzling out, his movement found itself with state funding and support. Other rulers realized they could follow suit, so the Calvinists and Anglicans got state backing as well.
With the introduction of state-backed denominations, there was suddenly a doctrinal free-for-all. The differences in Protestant denominational beliefs come from this situation. It's important to note that in the earlier three schisms, although there were specific points of disagreement, the overall understanding of things like how the Church is organized, whether the Sacraments are a means of grace, whether iconography is allowed, all of that remained undisputed.
With the rise of Protestantism, that was no longer the case. You had people as conservative (relatively speaking) as Martin Luther arguing that Communion is truly the Body and Blood of our Lord, and you had people as off-the-rails as Lelio Sozzini arguing against the Trinity. The Anabaptists in particular changed a lot of doctrines, arguing that only "believers" (i.e. not infants) could be baptized, that there were no sacraments or "ordinances" but baptism and marriage, that communion was entirely symbolic, and many other things.
It's hard to nail down what any one movement taught because there was so much variety. Anglicanism retained many of the beliefs of Catholicism but changed their understanding of church organization to put the king at the top and notably changed their rite of ordination, resulting in Rome no longer recognizing its bishops as valid.
Another movement, Calvinism, didn't originally start out as what we know today as TULIP/five-point Calvinism, but the acronym isn't a bad summary. In short, it teaches that we have no free will and are predestined to salvation or damnation. If we become Christians and are ultimately saved, according to Calvinism that's entirely the result of God choosing to save us rather than anything we do in cooperation with Him.
Lutheranism traditionally shares a lot of its theology with Catholicism, but obviously reduces the place of the Pope of Rome compared to Catholicism. It teaches that we are justified by faith alone, although from what I understand Luther included things like faithful reception of the sacraments in "faith" and didn't mean just nominal acceptance of Jesus as your lord and savior.
All of the aforementioned Protestant groups share in their reduction or omission of the practices of venerating saints and having iconography.
The Protestant Reformation was not started with the intention of endless schism, but it was the proverbial camel's nose under the tent. As doctrines like seventh-day adventism, women's ordination, homosexual unions ("marriage"), ordination of homosexuals, etc. gained support, it was all too easy to form a "party" within a denomination and start a new schism where you could go off and do whatever you want. This is why there are so many denominations today that trace their roots back to the Protestant Reformation, while successive schisms from the Church of the East, Oriental Orthodox, Eastern Orthodox, and Roman Catholics have been very few and far between.
