From the ones I can remember:
Pirates are invisible.
UI is even slower than before. Tooltips take longer to create. insynchOTC in stream was complaining that it was completly black and unusable.
Post-game report cannot be seen
Unconfirmed, but engineering labs seem slower than normal. It says 60 seconds, feels more like 80. IDK if it's jsut me or what. EDIT: after testing in single-player, the issue is that strikes make the timers change times wierdly. I could be 20 seconds from finishing an upgrade whilst striked, and it'll suddenly claim it'll take 120 seconds. Then when there's 105 seconds left it'll go back down to 5 seconds. Further testing shows that engineering labs and patent labs both actually research at the correct times, just that the timer above the building is incorrect, counting down slower than it shoudl be, even without strikes or adrenaline boosts.
Auto-supply is broken. Even when next to the base a building will spend about 5 seconds before realising it can buy the resources from the market to fill itself. It fills itself, then uses all the resources, then gets empty. Waits 5 seconds then realises it can fill itself. Rinse and repeat. God help you if during those 5 seconds you spend money. God help you as well if your using more than 1 type of building that needs auto-supply, because it seems that the more different types of buildings you have the longer it takes to realise ti can supply itself. This does NOT happen when your producing the resource your building is spending, unless you sell that resource. If you are not producing that resource however, your better off just turning off auto-supply. Also soren, I lied about being super clear
Patent and engineering labs, when boosted, don't reduce in time lineraly. It'll lower 1 second per 1 second, then jump down 2 or 3 seconds after a little while.