I had a similar problem in first beta.

I had a single shipyard and all my colonies were sponsors.
At some point of the game whenever I tried to enter the shipyard the game crashed.
The only way to make it work was to select a ship from quick build list and always postponing the previous one.

I just had a different experience.

Built a shipyard, assigned 5 nearby planets to it.

Shipyard got destroyed in battle.

Built another shipyard on one of those planets(not the one I built the original shipyard on, because for some reason I couldn't build shipyards there anymore).

Clicked the Add Sponsor button. <boom!> Game crash.

Loaded the game and attempted again, happened again, and again, and again, and then I got tired.

I Am 160 turns into a large map against 3 opponents and all my shipyards are bugged, even earth which has never been destroyed. I can build ships and. Everything, but if I click the add sponsor button the game instantly shuts down, have rebuilt them and everything, nothing works.

I can confirm also seeing the same behavior with the orphaned shipyards.

This is a know issue that has a fix for it in Beta Patch 2.

It's already out as an opt-in patch.