To invade a planet you first need to destroy any defenses on or around the planet.
Missile batteries, space stations, Ships, etc, if any or all of those are present the planet is considered defended and you cannot invade until they have been removed.
Sadly not true. I ran into a situation where a defended colony world was conquered by transports alone:
I had a little police ship in system for defense. Not enough to blunt a serious attack but enough to stop opportunistic raiders (or so I thought). The nearby Kor`Tahz being their usual a-----e selves decided to attack me. Their brilliant plan: send some unescorted transports. Well, easy peazy. My little police ship captain squares his manly jaw, gives a little speech about the power of justice, fires his lasers, and forces the transports to retreat. Victory! Right?
Nope. After the space combat concludes I see the planetary invasion screen. My baby colony is being invaded by the transports that JUST RETREATED! Whah? I reloaded a few times out of curiosity to examine the phenomenon. Turns out it was repeatable. Heck, I got it to happen twice in a row once (the brave bastards on the planet actually managed to beat off the first invasion once). Got the same results with the police ship orbiting and patrolling. Poor little guy just couldn't shoot down all the transports in the two turns it took them to retreat and the planet fell in the invasion phase.
The thing that kills me is that I'm not sure that anything was going wrong. I mean, is that what's supposed to happen? It isn't inconceivable that invasion ships could do an end run around a single defender and pull off some kind of lightning aerial invasion. Sort of the story of the game for me. I routinely ran into situations where I just didn't get enough information from the UI to know why something was happening.