Pantheism can be a tricky subject. There are no obvious logical fallacies with the idea of it, and being that the god believed in is not personal and not necessarily omnipotent. Pantheism means that God is a part of all of the universe, and dualistic pantheism implies that there is a spiritual world hidden beneath our physical world.
While there are no logical fallacies within the idea itself, the entire belief of it is unfounded and, to a degree, dangerous to scientific advances. There is no evidence that any part of pantheism could be true. I look at it as a sort of "god-of-the-gaps", living between the gaps of humanity's knowledge about our minds and the universe. At this stage in humanity, the gaps are small and the only reasonable form of a god is pantheism. But that is not how science and logic work. It is illogical to fill in gaps with such an idea. Pantheism is not a theory, it is a hypothesis at best; the result of an undying need for humans to believe in a higher deity. I will not pretend to understand this need, but I see that it is very common.
Filling in the gaps with this dualistic kind of god gives us an easy excuse to just give up on the difficult problems in science. If you take a look at the history of religions, God is used to explain a lot of phenomena that we now understand perfectly through science; things such as lightning, the sun, and disease were explained for a very long time as "spirits" and "gods". We should recognize this pattern and see that blaming a god on anything is eventually proven to be wrong.
What scientific problems am I speaking of when I say that pantheism could be used to cover the gaps in science? There are a few problems in physics that it could explain, but the biggest one is the human consciousness. The human consciousness is a very difficult problem indeed; one that is almost impossible for us to mentally conceive. It is very easy to just explain it as a spiritual entity and ignore it, but that gets us no where. The duality in pantheism suggests that somewhere in our brain is a link to the "spiritual" side of our universe, and that this is where all decisions come from. Free will is a very messy subject in science, and if we just say that it comes from magic then our brain suddenly makes a lot of sense. The brain just inputs its senses to the part of God that is in your brain, and God tells you what to do about it. Although the problem of consciousness is a large one, this is not the way to go about it. We cannot recreate this dualistic consciousness in a machine. Technology in this department ends here if this is where we stand, but the technology that could come from programmed consciousness is nearly infinite.
So while pantheism does not contradict with our science (yet) and is logically sound, it is still not a good replacement for the personal god. It is just as dangerous to science as any other kind of magical thinking. Comment and let me know what you think about all of this.