[Q]

Good evening TNTTony and greetings to Australia from Europe!

I think you speak about strategic combat because in tactical you can move first your attack ships into place and wipe out all enemy weapons. In strategic combat you have to set the fleet strategy to "capture planet" and to mark the box under "damage" in the empire strategy window "damage until all weapons gone" for this strategy. The secondary strategy for "capture planet" should be "optimal weapons range". In my experience this works in 95% well. Sometimes if the planet has a low population and few facilities and your attack ships have powerful weapons the Last shot that takes out the weapons takes out also the population and the colony is destroyed.
Hope this helps!