Here's a question that must be asked of any church claiming to be Christian: If I read the Bible and find something that contradicts your teachings, what do I do with it? Most churches, obviously, will claim you won't find anything like that in the Bible. They're obviously not going to flat out admit "yeah, the Bible disagrees with us on a number of issues". That's just guaranteed to discourage converts, and attract condemnation. But that doesn't actually answer the question. The question is if. "If" doesn't even assume you will, it's simply a hypothetical "what if" scenario.
We actually see several scenarios like this in the Bible. Elijah, for example, said to Israel "...If the Lord is God, follow Him; but if Baal, follow him." (1 Kings 18:21, emphasis added). Then we see in 1 Corinthians 15:12-19, Paul talks about what if there is no resurrection? What if Christ hasn't died and risen again? Neither Elijah nor Paul considered these scenarios to be possibilities, but they presented their "what ifs" regardless, and more importantly, they answered them. So bring your target back to the original question: If I find something in the Bible that contradicts your church, what do I do with it?
There are several answers you can expect, some of which are tied to a denomination, some of which are tied to the local church alone, and some of which are just individual answers. Whatever the source of the answer, there is only one valid answer: "My church is wrong. Go with the Bible."
There are a variety of denominations in the world today that claim exclusive rights to interpret the Bible. Jehovah's Witnesses, for example, will claim that there is nothing unBiblical about their Church, and yet they believe this entirely because they believe their Church holds exclusive rights to interpret (and translate) the Bible. And so the answer they will give is ultimately going to be if you find anything in the Bible that contradicts the teachings of the Watchtower Society, you have interpreted it incorrectly, or you're reading a bad translation.
Paul had no such quarrels. In 1 Thessalonians 5:21, he implored the Church at Thessalonica to test all things and hold on to that which is good. In Acts 17:11, the Berean Jews did not accept him outright, but searched the scriptures daily to test his claims, an act which Luke calls "fair minded". In Galatians 1:8, Paul even said that if he preached another gospel, even he would be anathema. If you asked Paul, or any of the other Apostles, "what should I do if I find something in the scriptures that disagrees with what you're telling me?", they wouldn't even blink before saying "resist us to our faces" (Galatians 2:11). If even the original Apostles expected you to test their claims against the scriptures, how much more should we test a modern church? The mere fact that some people don't want you to test their church or denomination against the Bible means they have already failed the test, and you can guarantee you will not be a well fed sheep should you take them as your shepherds.
Unfortunately, even the most Godly of churches will inevitably fail on occasion. If you go through the Bible and find one tiny disconnect, that's not grounds to dismiss the entire congregation as a bunch of heretics and storm out the door, kicking the dust from your feet as you do so. But there are scenarios in which it just makes no sense to keep attending a church. A low view of the Bible, or an arrogantly high view of another source, are very bad signs.