The only real problem is Reason. If we assume that a brain arose that then started to ponder on the world, then Reason cannot definitively exist.
For if logical propositions are only the product of specific chemical processes in the brain, than if those processes were different, then that would be logical. There is then no way for us to ascertain if something follows something else at all, since reasoning is dependant on processes that might just as well have been different. What we consider 'reasonable' might just be a product of our biology and not on account of concepts actually being related or conclusions necessarily following our specific axioms or thought processes. (Often we see different people coming to vastly different conclusions with the same data set, which actually supports this)
In this way then, if we accept the evolutionary origin of consciousness and reason, then we must doubt the very reasoning which we had used to accept the evolutionary origin in the first place. This does not of course mean our reasoning is wrong nor that evolution does not occur, but it does make all human knowledge highly suspect, if nothing else.