A few things I have run into, when in the pop-up window for giving ship commands, if you select something it can no longer do, (ie telling a ship to explore and there is nothing left to explore) another window pops up to tell you it cant do what you asked but that window stays buried under the window you are in so you do not see it until you close the original window.

There is a star system, it has four planets only one is habitable. Two are gas giants, one is a tiny mercury type fireball and the last is a earth like world. The habitable planet is not the earth type planet but the fireball, this really throws the game off for me. Also have seen many times earth like planets that are not habitable, this really should be addresed as it doesnt look/feel right.