I found these two hives stuck on the exact same spot. It looks like they are trapped in eachothers' tractor beams, or that they thrust just enough to cancel out the beams and get stuck or something. I don't know if this is a bug or not, but it is odd.

I don't think this is a bug. Or if it is, it's not clear to me at all what the bug is. They could just be sitting on top of each other, which ships will do, though it does look kind of broken in C2 and not broken in C1, since in C1 they stack.

I'm wondering if we should add a little something where ships "inside" each other will periodically generate a small force apart, kind of like if they were hit by a tiny mass driver, to nudge ships away from sitting over each other.

2 ways to fix this. you either put a collision code around the ship so the ships will simple bounce off each other (set the collision box/sphere out side the range of each ship). Also add a bank feature to the ship after colliding (this will give the fell of it turning away and not actuarially hitting).

For example if you had to ships coming together offset by a little bit. When they hit the collision code one would bank right other would bank left to avoid hitting.

second way is offsetting the ships on the z axis. so as they pass over they simply go above or below the ship they are passing over.

Yeah, if they functioned like magnets function it would be awesome. As two magnets of the same polarity get closer, the force pushing them apart gets stronger.