Quoted from squirtbrnr:
The same has happened on a planet wizard mode and occasionally I’ll start one of those with 3 balls instead of just 2.
This is sometimes normal - it depends on the number of modes your character had to complete for this planet - if the planet multiball is the 3rd mode (after 2 regular modes), the planet multiball starts with 3 balls. (They shouldn't appear in the shooter lane at the same time though.) If you're sure that this should just be a 2-ball planet multiball, then yes that's a trough eject problem.
There is a software bug that puts 2 balls in the shooter lane consistently under a different condition. It happens if you use an add-a-ball (which activates the ball saver) just as another ball drains - the ball-saved ball and the added ball both get served to the shooter lane before it plunges either. I wonder if this might also be happening at the start of TIE multiball, if you lose the original ball just as the ball saver activates.