Of all the conceptually confused areas in philosophy, philosophy of mind is probably the most confused. Think of, for example, mental causation, or the debates on the relation of brain states to mental states, or the causal relation of neurons to thoughts, things along those lines. The confusion, like all conceptual confusions, is a simple one.
Suppose one performs a scan of a brain and observes the patterns of neurons when a certain cognitive action, like thinking of a certain thing, happens – or observe certain areas of the brain lighting up when a certain cognitive action is undertaken. In short, the physiological processes that, more or less, make thought happen. This is a normal observation made every day in laboratories across the globe – the confusion arises when it is assumed that what is observed is mental causation (brain states cause mental states, or something of the sort).
Empirically, what is observed is not mental causation but mental correlation – as I’ve pointed out before, causality is a metaphysical, and not an empirical, category. Any notion of causation takes one, implicitly if not explicitly, into the realm of philosophy. If one supposes that all that is observed is all that there is, one has crossed from science into philosophy – whether or not it is done well is another story entirely.
(As a late edit, I’ll add that mental causation is more varied than what I listed here – for example, epiphenomenalism, which denies the mental any causal power – mental states are caused by brain states, but brain states are not causally influenced by mental states – is a big part of the philosophy of mind debates)
This shows, again, how intimate the connection between science and metaphysics is. Think of an intricate braid made of two different strands of rope. While they are two distinct things, when they are intertwined correctly, they form a strong, intimate bond, as opposed to being tangled together in a lump, which serves only to prevent it from being used properly.
While of a slightly different nature than the causal confusion above, it’s easy to see how other confusions arise – for example, that neuroscience has shown that free will is an illusion. This again is simply a muddle of confused thinking – certainly brain science has a lot to tell us about the mechanical/physiological aspect of human volition (it has, and will continue to, inform us more and more of the mechanical, but not mechanistic, workings of the brain), but it has very little, if anything, to say about human freedom seen as a whole, and not merely seen as volition (which has very little part to play in a full account of freedom).
Such are the perils of conceptual confusions.