I completed two transports of the same custom design in a turn. Only one ship completion icon showed (on the right side). I checked which planets completed ships by using the planet list with the sort set on military turns (I also have "Build same ship until canceled" off). I selected one of the two planets that had just completed ships (single click) and used the starport button at the bottom of the main screen (shows up only when a planet is selected) to go directly to the starport and select another ship to be built, then pressed the "done" button. Then, from the main screen, I selected the transport and clicked "launch", got the ship loading window, filled the ship, and clicked the "launch" button on the ship loading window. I immediately got another ship loading window. I filled the ship again (at least that is what I thought I was doing), and launched it again. Now I have only one of the two ships available and I can't figure out what planet completed the other ship.
Occurance rate: only once so far.