Spoiler tags don't seem to work in my client, so beware if you have only just started the books or tv series, or wish to not have your suspension of disbelief broken

That plot line is closely related to the biggest plot hole in the books and tv series

Sophons are sent to Earth at near light speed, presumably accelerated in a particle accelerator. They are the size of and very like protons. In fact they are protons that were unfolded, had AI computer logic etched into them, and were then refolded. How would they slow down? How would they change direction? Note that they are shown to turn within a fraction of the radius of a retina and hardly interact with matter at all.

A proton takes a fair bit of energy to accelerate to a high fraction of light speed, and just as much to stop or turn.