What is the most unintuitive physical fact

Zeno (around 500 BC) put this paradox in a nutshell to argue against the notion of "plurality", arguing that this is a belief in the existence of many things and not just one leads to absurd conclusions: If there are many things, they must be both small and large; so small that it has no size, but so large that it is unlimited.

See section 2.2 of Zeno's Paradoxes in the Stanford Encyclopedia of Philosophy. The following quote is from a discussion of Zeno's book on Paradoxes by Simplicius (who apparently still had his book a thousand years after Zeno, which is now being lost):

If a thing had no size, mass, or mass, it would not exist. Because if it were to be added to something else, it wouldn't make it any bigger. If it's not sized and added, it can't get any bigger. And so it immediately follows that what is added is nothing. But when it is subtracted the other thing is neither smaller nor enlarged, when it is added the thing added or subtracted is clearly nothing.

This seems to be the earliest source of the paradox, but not its resolution, which had to wait several millennia for the concept of a distance function to develop that allows you to compute the length of an innumerable infinity of points.