LED lighting can "wreak havoc with the internal body clock of nocturnal animals." I am skeptical.

Does this phenomenon occur because of the difference in the index of refraction of the media? Does that same phenomenon also occur in the eye with whatever the light has to pass thru before being turned into an electrical signal? If so, does that mean we often get chromatic aberration with the naked eye, it’s just too slight in angle and intensity for us to notice it?

Yes.

That is my understanding. On-axis (at the center of your eye’s field of view), the aberration mostly manifests as softening of the image, but it is a small effect. (Though this may be one reason why it’s hard to read writing in purely blue or purely red lighting. Though that has more to do with the green cones being more sensitive than red or blue.)

Off-axis (away from the center), the retina has much lower resolution (lower concentration of receptors), so it’s not very noticeable. Also, the brain can correct for it to some extent. Off-axis, chromatic aberration causes blue light and red light from the same source lands at different points on the retina. It’s a consistent offset so the brain just knows which blue cones and which red cones correspond to the same place.

Modern cameras actually do the same - in addition to the lens itself being designed to correct for chromatic aberration, the image processing corrects for the residual chromatic aberration by shifting the red/blue pixel signals slightly.

Disclaimer: Optics is my specialty, biology/medicine is not.

If you’re using your cell phone to call me at that hour of the night, you’d certainly be causing sleep issues at my house. Who do you call an hour before bedtime?

These days, phones can do things other than call people.

Blue light suppresses melatonin production, the hormone that regulates sleep. Here’s a Scientific American article on the subject (The Daily Mail is indeed clickbait swill, especially their science coverage, but even they pick up on genuine issues from time to time.)

In my personal experience avoiding bright and blue light late at night has made a huge difference to my sleep quality. It now usually takes me a few minutes to get to sleep instead of an hour or more. I use f.lux on my PC and eye comfort mode on my phone and tablet, to dim and redden their screens.