There are things that are "right" - the scale of the solar systems and universe as a whole, for example, and the way (most of) the planets move around in their orbits, and the way a space station goes into darkness when it moves into the shadow of the planet it's orbiting.
There are things that are "probably right" - the colours of alien planets, for example, can be extrapolated based on what we know of physics and chemistry.
There are things that are in the "we don't really know, so FD's guess is as good as ours" - such as the long-term stability of binary giant planets.
There are some things that have been "hollywoodized" for visual effect and/or ease of gameplay. The three biggest in this category are nebulas (IRL they're much dimmer and less colourful), asteroid belts and rings (IRL they look much less star-wars-like) and the centripetal pseudo-gravity inside the rotating space stations (IRL there's no law of physics that allows a spaceship not attached to a spinning object to just hang there and rotate around along with the rotating object).
There are some nit-picky things that are just plain "wrong". Ages of stars, for example, are uniform cross a star system - including T Tauri stars. In reality, stars in binary and multiple star systems probably light up at different ages, particularly ones in eccentric orbits.
The procedural generation of stars is in "blocks". This block will have a large proportion of black holes and neutron stars, the next block might have a high proportion of giants and supergiants. This leads to a "lego-like" galactic structure, which is actually visible in some places: if you fly to the edge of one of the blocks, the night sky from there looks clearly assymetrical, with one side of the sky empty of stars and the other side ablaze, and a clear sharp line between the two. The real galaxy might have regions where certain star types are common, but won't have clear, sharp lines like this.
In places, we know where some "strings" of remote real-world stars are, and some of these strings have been placed on the ED galactic map. These "strings" are not physical, but are artefacts of whatever satellite or telescope took the pictures of that part of the sky. When these "strings" are denser than the procedurally-generated galaxy, they can create "rays" of stars, that seem to point directly at Earth - as if the Galactic Designer has built a vast supergun and was aiming it right at us. In reality, the star density outside of the "ray" is almost certainly exactly the same as the density in the "ray". There's one over near the Orion Nebula, if you want to see what we mean.
They haven't yet implemented universal gravity: our spaceships are immune to its effects. Moons orbit planets, planets orbit stars, but you can't "put yourself in orbit around" a planet. This is mainly because of the ridiculously low speed limits while flying in normal space (ie not Supercruise). At those low speeds, everything would simply fall out of orbit. In most places, this isn't really noticeable, but if you get up really close to a black hole (like, only a few km away from it) you don't orbit it, you don't get torn apart by the extreme gravity - your ship just hangs there, floating, not even using the thrusters to hold itself in position. I don't know what gravity is going to be like in Horizons.
New Africa in the Epsilon Indi system has a moon with an orbital period of 86 seconds. That's really moving fast - visibly fast, you can watch the moon go round and round from the safe distance of the space station. It looks cool, but we've done the maths and it's quite impossible for a "normal" planet to have a moon like that; a moon at that visual distance should have a period of at least an hour or two. I suspect there's some kind of over-ride to prevent moons from orbiting through the surface of their parent planet and a moon with an impossibly small orbital radius is given a more reasonable one when the moon is drawn, but the calculations of orbital speed are still done using the original numbers.
In real life, planetary rings are not solid objects - each particle is its own moon and ring particles closer to the planet move slightly faster than ones further out - like cars on a giant circular million-lane freeway. But the rings in ED are, effectively, solid objects, albeit solid objects you can fly through. Just as if all the cars on the road were superglued in place and the road itself was moving, the ring particles are all magically attached to this invisible solid object, and rotate with it, so every particle in a ring has exactly the same radial velocity - which in turn means that the ring particles on the outermost parts of the ring are actually moving faster than the innmost parts, rather than slower like they do in real life. A spectacular side-effect of this is when you fly up to a ring boundary, you can look across at the next ring in (or the next ring out) and watch the particles in that other ring whiz past at super-high speed.
Overall, the physics is good, and easily allowing me to "suspend disbelief". But it is by no means perfect.