When I send a ship to a planet that is above or below the plane with the majority of the planets, the ship will fly around the no-jump zone for a long time. I was unable to reach one planet at all. Some of these planets work more or less normally.

Another planet was stuck half inside another planet, I almost didn't notice it until I saw enemy trade ships appear out of nowhere. I was able to get to that planet with one ship, but I had a capital ship trying to jump to it for over an hour.

This was on a custom map with 1 star, 3 planet clusters. The cluster with the offending planet was a random mix of 10 planets, and pretty much all of the other sliders set to the left, which I will assume is equivalent to "least". Patched to the newest version as of 4/24.