A number of philosophers argue that consciousness cannot in principle be explained by materialist/physicalist methods. They believe that subjectivity is not amenable to a physicalist explanation.
I self-identify as a Christian materialist, which means that while I believe spirits exist (God, angels, and resurrected spirit beings), I do not believe in immortal souls nor do I think the human sphere contains a "mental" or spiritual component. In other words, I reject the existence of an immortal soul or a res cogitans as Rene Descartes famously expressed matters. It seems that humans are purely physical: we do not have non-material souls or spirits.
Scientific work is just beginning (in earnest) on questions pertaining to consciousness and subjectivity. The neuroscientist Antonio Damasio has written books that possibly attempt to integrate free will and a physicalist account of the self. He and Hanna Damasio (along with many others) have extensively studied the case of Phineas Gage, and what it might tell us about mentality. See Descartes' Error by Antonio Damasio. There's also a book that I'll start reading soon entitled The Neuroscience of Freedom and Creativity: Our Predictive Brain written by Joaquin M. Fuster (Cambridge Press). Joel B. Green has also published works that partly analyze the role of brain activity in our mental life. Admittedly though, much work needs to be done in this area. But I would not agree that science lacks the resources in principle to explain memory (for instance) or pain in physicalist terms, since joint pain could be explained by the overabundance of uric acid or the wearing away of cartilage.
Long-term memory can be explained by the hippocampus or the fight/flight response could be explained by the amygdala. As for free will, Nancey Murphy addresses that question. She demonstrates the possibility that free will could exist even though we might be purely material beings. Physicalists have worked on qualia too, with no definitive result. It's still an open question just what qualia are. Almost every writer that I've read in the philosophy of mind accepts the existence of qualia. However, there's no unanimous consensus respecting how we experience "raw feels" or subjective sensations. Does dualism fully address this question? Not to my knowledge. Dualism offers suggestions for how mentality works, just like Christian physicalism does. Neither approach definitively explains consciousness.