What If I Have Difficulties With The Present Day Christian Church?

Before I began to study scripture with spiritual discernment I never had so many objections and questions about what is going on in present day christian church. When I just attended church and listended to the minister and did not study, I had no issues. The more I read scripture, the more I disagree with what is being preached in many the present day christian church. At times it appears religious theology contradicts God given scripture. Is there something wrong with me?