But though animals learn many parts of their knowledge from observation, there are also many parts of it, which they derive from the original hand of nature; which much exceed the share of capacity they possess on ordinary occasions; and in which they improve, little or nothing, by the longest practice and experience. These we denominate Instincts, and are so apt to admire as something very extraordinary, and inexplicable by all the disquisitions of human understanding. But our wonder will, perhaps, cease or diminish, when we consider, that the experimental reasoning itself, which we possess in common with beasts, and on which the whole conduct of life depends, is nothing but a species of instinct or mechanical power, that acts in us unknown to ourselves; and in its chief operations, is not directed by any such relations or comparisons of ideas, as are the proper objects of our intellectual faculties. Though the instinct be different, yet still it is an instinct, which teaches a man to avoid the fire; as much as that, which teaches a bird, with such exactness, the art of incubation, and the whole economy and order of its nursery.
(From Of the Reason of Animals.) What's puzzling about this? Hume rejects the doctrine of innate ideas. We also know he tends to interpret that pretty broadly, so that, for instance, one of his criticisms of Thomas Reid (in the letter to Hugh Blair) was that Reid's position "leads us back to the doctrine of innate ideas." But this talk of knowledge derived from "the original hand of nature," of which we have an instance ourselves in "the experimental reasoning," seems itself to be leading back to the doctrine of innate ideas. I suspect that the difference, as Hume would see it, is that our mind's natural operations are "not directed by any such relations or comparisons of ideas, as are the proper objects of our intellectual faculties"; that is, this instinctual knowledge cannot be understood by innate ideas because we never perceive the ideas: it works "in us unknown to ourselves." Hume, of course, wouldn't deny that there are "secret springs and principles" in the mind; and these would certainly be different from ideas in the Humean sense of the term. Nonetheless, it is noteworthy that the rejection of innate ideas does not involve the rejection of innate knowledge.