If you don’t already suspect it before reading Scienceblind: Why Our Intuitive Theories About the World Are So Often Wrong, we humans are often very, very ignorant and wrong about the way things work. The author takes us, chapter by chapter, through physics and biology and shows that, at every age, we fall prey to preconceptions and plain misunderstandings of what we supposedly learned. (He is very kind and gives us examples of confused graduate physics students so we don’t feel so bad!)
He also tries to lay out recommendations for how to bridge the gap and is less successful at that (for one thing, his specialty is psychology, not physics or biology). Still, it seems that STEM courses should spend a little more time contrasting the truth with common preconceptions rather than just solving equations. The problem seems to be the intersection of “common” sense and technical knowledge.