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Set in the near future a spaceship flew across an unclassified region of the Milky Way galaxy and found a Super Earth in an unnamed system, the planet is almost twice as massive as Earth and is orbiting fairly far away from it's parent star. Unfortunately there is no liquid water and is deemed too cold for settlement, strangely one side of the planet has a gigantic flat ice sheet covering half of the planet surface while the other side is ridded with craters some as deep as 20km below global mean surface gravity level. How to explain the finding?

I'm reminded strongly of Iapetus, a moon of Saturn that has a dramatic two-tone coloring. One hemisphere is quite light, while the other is dark. It almost looks like you dunked half of the moon in chocolate:

^{Image credit: NASA/JPL-Caltech/Space Science Institute/Lunar and Planetary Institute. Public domain.}

Iapetus is tidally locked, meaning that one side is always the "leading" half of the moon. This means that it easily attracts particles from a giant ring of dust created by the moon Phoebe, which orbits in the opposite direction. One half of Iapetus is bombarded by the darker particles, which, a long time ago, kick-started a feedback loop that sublimated ice on one side while keeping it frozen on the other. This self-propagating cycle continued until one hemisphere was dark and one was light.

I can imagine something similar happening here - tidal locking in the past, and a transfer of material from another planet orbiting close by in a retrograde orbit. It's possible that this transfer could have been a true bombardment, rather than the light dusting Iapetus received.

Big impact.

Something like this might have happened to Mars.

https://www.space.com/5558-huge-impact-created-mars-split-personality.html

Scientists have been scratching their heads trying to explain the differences between the two sides of Mars for about 30 years. The northern hemisphere of the planet is smooth and low, and some experts think it may have contained a vast ocean long ago. Meanwhile, the southern half of the Martian surface is rough and heavily-cratered, and about 2.5 miles to 5 miles (4 km to 8 km) higher in elevation than the northern basin...

"What we noticed is that the dichotomy boundary around the planet was actually smooth and regular. We tested to see if we could fit this with any shape, and it just so happens that it's almost perfectly fitted by an ellipse. There's only one process that's known to make an elliptical depression like that, and that's a giant impact."

So too your planet. Something big whacked into it hard, flattening out the water side. An impact like that probably softened everything up, and when it equilibrated the new giant hole filled with water, that then froze.

Whatever the big impactor was, it had friends which accounted for the holes on the far side. Or maybe material knocked free from the impact flew out and then eventually back in, digging those craters on the dry side.

Just a shot in the dark, but the planet could be tidally locked, similar to our moon, meaning that one side always faces away from the sun. It could be that the side facing away from the sun would have cooled so much as to create a frozen surface of water, while all water from the other side boiled away. The craters on the inner side are caused by meteors, and they show only because there is no frozen ocean covering them, only bare crust.