In my current game, the Command Ship had 3 hitpoints remaining and a technology for adding a build slot was being researched. The following events happened in rapid succession:
1) I selected two planets to play and ended phase.
2) As soon as the Combat points were collected, I shot the Command Ship boss three times. Wellness points were being collected at this time.
3) The Science points were collected, finishing the technology and presenting me with the option to add a building slot to a planet.
4) Less then 1 second later, the animation to destroy the Command Ship completed and the game presented me with the option to select a new planet. I had not yet selected a planet for a new building slot.
5) I selected the new planet. The option to add a building slot was gone.