My main complaint is you can colonize a world with a mining station in orbit, and the station is just destroyed in the process.
I had a desert world with korabban spice one system over from my homeworld in one game, but it was below 50 quality and thus wouldn't really be useful as a colony - so I made a big custom station there with massive luxury mining capability (way more than a colony could do) and lots of cargo bays and docking ports and a huge arsenal of weapons surpassing even my large space ports. I planned to use it to supply my entire empire and those of my allies with korabban spice. It was working great, shipments of the stuff were going direct to the homeworld and I was just overflowing with it and all my colonies were reaching 130 development.
Next thing I know the system is colonized. I go there and my allies the Securans (we have a mutual defense agreement) have colonized the planet. A completely unarmed colony ship flew in and took over a planet that was supposedly guarded by a heavily armed station, and in the process destroyed the station.
I had to declare war on my allies to get my planet back, and in the process got a bad reputation and ruined my relations with my best trading partner. Plus now that its a colony instead of the giant station im actually getting less spice, and you can't add more mining capability to a colony.