Yes, there were disputes over several New Testament books, known as antilegomena. These included Hebrews (authorship questioned), James (seemed to contradict Paul on faith/works), 2 Peter (style differences), 2 & 3 John (brevity and authorship), Jude (references non-canonical texts), and Revelation (apocalyptic nature). Early church fathers like Eusebius noted these debates, and figures like Marcion excluded many. Consensus formed by the 4th century via councils like Carthage (397 AD), though some variations persisted regionally.