I was affected by this as well and I believed that I have pinpoint the source of this bug. It was caused by launching a colony/transport from a planet with less than 0.5 population, since 0.5 is the minimum that is required to load the colony/transport ship.
In previous patches, this bug doesn't occur since there is no way to own a planet with less than 0.5 pop. But, in 0.50, there are two methods that you can achieve that. First, when you buy a colony ship from the AI, the pop of that colony ship will be reduced to 0.1. This is likely done to reduce the impact (read: abuses) of player keep on buying colony ships from the AI. Secondly, when you hurry a colony ship from a shipyard with a planet sponsor beyond the natural shipyard distance (i.e. 100 tiles away), the colony ship will spawn with 0 pop. This change is done to prevent the abuse noted in previous patches, that a player can send pop from their old mature planet to a new planet in just a turn. Either way, it resulted in a colony ship that can colonize a new planet with less than 0.5 pop (Yes, you can colonize a planet with the 0 pop colony ship).
The bug occur when you send another 0 pop colony ship (or transport) into the new <0.5 planet, and then tried to eject the ship. Since the pop of the planet is <0.5, the game will prevent the ship from being ejected and the prompt will keep on occurring regardless of whether you click Done or Cancel button. You will need to kill the game when that occur.
Alternatively, you can tried to rush a shipyard for the <0.5 pop planet, and then rush a colony/transport ship. The same bug will also occur.
Trivia: I've tried to invade an AI planet using a 0 pop transport. I've lost. 
Edit: It seems like I've found another bug. I've just doublechecked my game and for the first method, the bought colony ship wasn't reduced to 0.1. It was 0 to begin with. Some colony ships I've bought is 0 pop, and some are properly staffed at 2.5 pop. Since most of the 0 pop colony ships are stationed right next to their shipyard while the 2.5 pop colony ship are in the middle of space, it seems like the 0 pop colony ship was bought before the AI managed to eject the ship in the first place.
