On p. 226 of their book, Reasoning from the Scriptures with the Mormons (Eugene, Oreg.: Harvest House Publishers, 1995), Ron Rhodes and Marian Bodine argued that the Book of Mormon is in conflict with Latter-day Saint theology, citing Alma 22:10 and Alma 31:15:
And Aaron said unto him, Yea: he [God] is that Great Spirit, and he created all things both in heaven and in earth. Believest thou this? (Alma 22:10)
Holy, holy God; we believe that thou art God, and we believe that thou art holy, and that thou wast a spirit, and that thou art a spirit, and that thou wilt be a spirit forever. (Alma 31:15)
According to Rhodes and Bodine, the Book of Mormon explicates an incorporeal God, in opposition to D&C 130:20 and defined Latter-day Saint theology. However, just as Rhodes and Bodine are guilty of eisegesis in their treatment of various biblical texts (search this blog for previous discussions of their work), they are also guilty of eisegesis of the Book of Mormon.
With respect to Alma 22:10, the use of the phrase, "Great Spirit" was Ammon's way of communicating the concept of God to someone who knew deity as "Great Spirit." Furthermore, the people mistook Ammon for the Great Spirit, notwithstanding the fact he was clearly corporeal (see Alma 18:2-5, 11)! Obviously, use of the phrase does not preclude God being corporeal.
With respect to Alma 31:15, such a verse is part of a prayer of an apostate group, the Zoramites, and is not a reflection of the theology of the Book of Mormon prophets themselves so to claim that the theology of the Book of Mormon is in conflict with Latter-day Saint theology about the nature of God is a non sequitur. It would be similar to arguing that the Gospel of John denies the virginal conception and birth of Christ as the Jewish opponents of Jesus believe Joseph to have been the biological father of Jesus (John 6:42)! Of course, that would be a nonsensical reading of the Gospel of John when read in context, just as the charge made by Rhodes and Bodine is nonsensical and reflective of an ignorance of the Book of Mormon text itself.