First off, the Dread Lords still show up as an opponent. I had disabled them on a previous game, but I guess it doesn't stick.
Second, the second medium ship hull from the top is screwed up. Try to put things on the little nose wings, and they show up on the back. If you had something on that spot before, it is replaced.
Third, when I chose neutral, the red tiles on my planets did not become available. However, a class 12 world showed up as class 20 in the colony view, even though counting all the red squares still only got me to 16.
I am playing tough, but the opponents still do some very strange things. Minor races fill their entire dock with freighters and constructors. Minor races also appear to be unable to form fleets. The Jessuins actually had 4 fighters flying around in a group, but the Drengins were able to destroy them one by one. Almost everyone declared war on the Drengin, which gave them a massive (but thankfully low tech) fleet. The next turn, three of the races surrendered to other players. Obviously no-one had met the Drengin fleet yet. Several races ended up in corners and did nothing. The Arceans ignored 4 asteroid fields two sectors from their homeworld.