I think I've found two bugs.
I was stablizing a jump point as well as a Lagrange point of Neptune, and I think they each did something wrong. First the Lagrange point is in the wrong place. I expected it to be 60?° ahead of or behind Neptune, but instead it looks like it is 120° away. It's LP2 in this screenshot, on the right-hand side of the orbit:

I was also stabilizing JP2 to HH Andromedae, and when it finished I sent a cargo fleet through with infrastructure. That worked ok, but it turns out that they're stuck there; the jump point back isn't stable.
All the civilian ships are now in the process of making the same mistake:
