I posted this in the sticky as well, but I wondered if anyone else has seen this, or knows what maybe be causing either of these.
Invasion bug:
The Invasion bug with defender ships in orbit is still in this version. I reported this bug in 1.0X, and hadn't seen it again until last night. Here is what happened:
I went to attack an AI world with a fleet that included a transport. Instead of fighting the defending ships in orbit, the screen went directly to a traditional invasion screen, completely bypassing their defense.
(This seems to happen only when attacking a race that you are not at war with. In other words, when this attack is the one that declares war on the other race.)
Upgrade bug:
Upgrading trade ships has taken away the option to put trade, constructor, or colony modules on the ship. What's more; it also gives me a free trade module on the ship, so that it has no cost or weight. This lets me load it with many more engines or lifesupport modules than I normally would be able to.
You can reproduce this by loading up a game, or starting a new game and open a previously built trade ship and hit the upgrade button. It will take off all modules, but act like the trade module is still on the ship. Load it up with whatever you want, and send it out to create a trade route, and it will work - without adding a trade module.
Both of these bugs occured on a "tough" difficulty level, in a metaverse game (using 1.1 beta 2 build 010). I have the save game for both of these bugs, if Stardock would like it.