Hello, I was not able to reproduce this and believe this is by design.

I landed 3 transports on the planet. I clicked Eject all because I have 3 transports, I had 3 boarding dialogs where I had to assign a citizen to the transport. I pick the citizen and clicked next for all 3. All three transports ejected.

I repeated this by landing the transports again with other ships. I selected all three transports in the UI while holding the shift key and then right clicked a destination outside the planet. I again had to board those three citizens.

That said if your trying to send out an empty transport the game will not let you. It will allow you to click Next and Done to skip assigning the citizen but will not eject the ship. This is intended.

If your trying to move population around you can use the civilian transport feature or you can make a transport with a colony module. Only 1 citizen is required for the ship so you can move 2 citizens and eject with 1 pick up another and repeat. Before the civilian transport feature this was the only way to shuttle population around without destroying the transport.

I was trying to switch the soldier in the transport to use a captured citizen.

Originally posted by Aurican:

I was trying to switch the soldier in the transport to use a captured citizen.

Try to make the Soldier a Cit and the Cit a Soldier
The Cit will have to be a soldier to load but that change should be Automatic

Issue is that the loading/unloading + citizen <-> soldier switching works when I am ejecting just 1 transport but not when I try to eject multiple transports at once.

Originally posted by Aurican:

Issue is that the loading/unloading + citizen <-> soldier switching works when I am ejecting just 1 transport but not when I try to eject multiple transports at once.

Are you double clicking on each citizen and moving them over for each transport?

Yes, no responses. Only response I can get are the cancel and next buttons. Suspect the wrong dialog has captured the mouse input.