Reply #1 Top

Yeah that's a rare glitch. If you want to share a save file over on discord we can add it to a bug report which will shine more lights on it.

Reply #2 Top

Your instinct is right, a shipyard is meant to settle on one supporting world rather than two, and it picks the nearest one.

That pairing gets recalculated when a world's status changes, so if either of those planets gained or lost core world status around the time you noticed it, that is worth mentioning along with the save.