It always bugs me when optical illusions are brought up as instances of failure of the our perception system. These contrived conditions are really the 'exceptions that prove the rule:' our visual system has powerful inference capability running below the level of conscious perception, and most of the time it works so well we can't fathom the distinction between the model we infer and the sense data that the system works from. For instance, we perceive one scene with depth, when what we start with is two scenes with slight discrepancies.

Somewhat tangentially, I recall a psych paper where the researchers found that people perceive images in mirrors to be located behind the surface of the mirror. The researchers apparently thought that the image was at the surface of the mirror (ie, they misunderstood basic optics), and concluded that they'd discovered an optical illusion.

Yes - humans do it abductively, which isn't rigorous but serves our purpose most of the time. You can't trust a self driving system with abduction though - it's the style of reasoning that gave us rain dances and homeopathy.

Nowadays yes. For most of history though (and still commonly today), causal explanations for plenty of things involved some flavor of the supernatural.

David Hume perhaps? He reasoned that causality was not empirical and therefore was a habit of thinking humans acquired from constant conjunction of events. Kant was troubled by that so he elevated causality to a category of thought, like space and time, which the mind used to structure sensations.