Sometimes it'll forget to tell you that you have units to move, you getting the NEXT TURN message in the bottom right corner of your screen. Workers, Explorers, Colonists, ships, etc., are sometimes skipped over, even when they aren't resting, and just moved the previous turn.
Some quests involve building something in a specific city that requires a resource that city does not have in any of its workable tiles. My Capital is supposed to build a Petroleum Well, because there is some Petroleum off in the ocean to the left of it. But no tile extends that far, nor am I able to buy that tile. It's been there for a hundred turns now. Also, I cannot build a Neurolab, or whatever it is, in a city that doesn't have Firaxite deposits near it at all, since you need that resource to produce the facility they want.
AI leaders will criticize you for being a warmongerer, even if it was someone else that declared war on you. They will not criticize this other faction though.
The ancient tomb quest can cause the ancient tomb to appear in enemy territory where you can't get to it.
Even in areas you haven't explored yet, you can see a number at a spot, showing you how many aircraft another faction has in their base there.
You can click on a plot of land that has one price listed, and then another price appears.
Sometimes when your agent steals Science, you don't get those points. If your agent finishes stealing Science points the same turn you get a new research (having only one turn left to get it the previous turn), then those stolen Science points just disappear.
Sometimes someone will criticize you for something you didn't do, such as attacking a station they were trading with, even if you haven't attacked any stations except one over a hundred turns before.
The rest and heal button does not appear for workers inside a city, nor do they recover any health if in sleep mode inside a city. You have to move them outside the city tile to have that button appear.
Even if you select a Domination only victory, you still have the game end with a Time Victory at turn 330. You can then select to play "Just One More Turn", and of course play far more than just one turn.
There is a major exploit with the trading and favors system. When an AI player asks you for help such as offering you 1 favor in exchange for some resource of yours, or a proposal of an open border agreement. After the deal expires, if the AI wants to renew the old trading deal with you, you can change or add the amount of favors they owe you to the maximum of 9999, and they will accept the new deal regardless. This will allow you to buy every city they own except their current Capital with the huge amount of favors you just acquired.
During the "Written in Stone" quest, the ancient tomb will despawn the turn it is created, preventing you from both settling and using that tile. The ancient tomb will still be on the tile, but you will be unable to excavate it. Reloading from a previous turn will not help either. The tomb will just stubbornly sit there, refusing to despawn and preventing usage of that land.
Sometimes station improvements or resource markers will not despawn, causing the resource or station to appear on the tile without affecting the tile.
Capital is supposed to build a Petroleum Well, because there is some 
Petroleum off in the ocean to the left of it. But no tile extends that far, nor am I able to buy that tile. It's been there for a hundred turns now. Also, I cannot build a Neurolab, or whatever it is, in a city that doesn't have 
Firaxite deposits near it at all, since you need that resource to produce the facility they want.
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