Got a few things to say here, apologies if they've already been said before. Enemy AI commanders don't repair themselves Enemy AI repeatedly nuke the same location where a base formerly was Buildings can be placed in craters of planets that have had moons hit them, but the buildings do not meet the new topography and hover in the air Numerous pathfinding problems; if a unit is surrounded by multiple idle units it does not always push through and remains trapped. Spinning seems to be another peculiar issue. On using the Annihilate menu, you lose the top bar containing your resource stats Construction issues; some buildings become only half constructed (Commonly seen with orbital construction units) or only a blueprint appears and no build progress is achieved If moon orbit is too close to the planet, there can be issues where your orbital units cannot leave the pull of the planet to access the moon That's all that comes to mind recently
Another bug (sorry if already mentioned elsewhere): The AI tried to expand to the 2nd planet quite early in the game. It sent a normal land fabber but the planet was more water than land and the space transporter (I forget the name) just sat above the water for the rest of the game holding the fabber. The AI never expanded there even though the game continued for another 20+ minutes. Though it was more sea than land there were several reasonably sized land masses it could have landed on.