This is a game I started before the patch and continued to play it with the opt-in patch.
1. In the sponsor list for a shipyard a planet is listed incorrectly, this one only has Earth and Mars, yet Devoa III is listed instead of Mars. In the shipyard manage screen the planets are listed correctly. I recall removing and adding planets as sponsors to the shipyard Devoa III belonged to, so that might have something to do with it.
2. On the mini-map there appears a very thin gray line. It looks like a line from a graph.
3. This bug has to do with the fact that you can queue multiple improvements that are Wonders, I set multiple planets to build Missionary Center, which is a Player Wonder, multiple of them were completed. After one was built it disappeared from the Improvement list, however if I destroyed one it appeared again.
4. Sometimes I could see the lines that connect shipyards to planets through the fog.
5. I'm not entirely sure of this one, when I unlocked a tier 3 bonus from the Pragmatic Ideology the points weren't deducted, when I unlocked the second one they were.
6. Logistical Support does not unlock anything.
7. I wish it was easier to tell how many starbases can be built without paying, and how much it would cost when building one over the limit.