This does exist to a certain point today, and always has. No one can honestly say, (if they study on their own, and think for themselves) they believe everything that their pastor or denomination teaches.
I, being a Baptist cannot say I agree with everything that the Baptist church teaches. For example, I believe in the availability of spiritual “sign” gifts today (speaking in tongues, healing etc.). But for the most part, I agree with what my church teaches.
The problem you are talking about here stems much deeper than individual differences, right into the problem of denominations themselves. With the start of denominations we encountered sects starting that would not even to today that people cannot cross, without fear of being ostracized.
Usually though, history will show us what caused these problems is religion itself. In every instance that Jesus spoke of religion it was in a negative form. When we start to concentrate more on what the church we attend teaches, on what the name of our church is, we lose focus on Jesus.
Today, we need to put our focus back on Christ, and try to be a Christian. Not a Baptist, Pentecostal, Catholic, or whatever. We first need to unite under Jesus.
Grace and Peace to You!