Ok so i got 3 more issues to add to the general issues list.
1.) You can incorrectly build oil derricks on burning oil wells, by telling your builder to build an oil derrick on a burning well, then saving and reloading and the builder will then incorrectly commence construction even though the oil well is still burning, as you can see in this screen shot.
This doesn't seem to be level dependent you can do this on any level.
2.) When you have more then 1 commander selected and you for example tell them to hold fire the hold fire state will not be applied to all the selected commanders and you will have to do each one individually, the same holds true when you for example have 3 commanders selected and you click to recycle only 1 will go, the same thing happens when you for example have say 3 commanders selected and then change the retreat state it will not be applied to all 3 commanders and you will have to click each individually.
This is incorrect behaviour when you have more then one commander selected what ever command you give should be applied to all the selected commanders you shouldn’t be needing to issue the same order multiple times to each commander individually so this is something that needs looking at because its kind of irritating and makes working with multiple commanders more difficult then it should be.
3.) When you target say a wall and order your units to fire your units will only fire the number of shots required to destroy the target, however when removing feature objects to avoid pathing issues this is not the case and all your units will fire at the target instead of just the 1 or 2 which are actually needed to destroy it, so again this is something else that should be looked at, because this is something that wastes a lot of time.