Tons of these in physics. Here's a couple.

People often say "hot as the surface of the sun" to indicate extreme temperature. But the surface of the sun is actually weirdly cool (~5800 K) in comparison to the area surrounding it. This area (known as the corona) is MILLIONS of degrees hot. And we don't know why. It's called the Coronal heating problem.

Another fun one is called "The axis of evil", and it is the observation that the most universal base of reference we have, the cosmic microwave background radiation—literally the remnant photons from the earliest time of the universe we can see (because before that, everything was opaque and weirdly orange), this background is completely aligned with our solar system. It's called the axis of evil because we're supposed to be insignificant, arbitrary, statistically randomly aligned. But this most basic yard stick is perfectly aligned with us. We also don't know why. A fluke, we must assume. But pretty evil, from a copernican perspective.