1.08 bugs.

[Raapys]

You did it in a seperate attack from the main battle?

I've only tried a few capture-planet attacks myself, and all the times I let the AI do the actual battle, just having a 'capture planet' strategy on my cargo ship. All those worked fine: the troops were deployed, combat started the next turn.

Perhaps the bug is that you, I assume, had fighters in the cargo ship with which you 'captured'?