Two bugs continue to plague Galciv2 in its latest version. The first is relatively easy to spot and I'm sure others have brought it up. Virtual reality centers continue to provide less of a morale effect than their predecessors (zero-G sports arenas). This is a fairly annoying mistake. Its extremely damaging to "accidently" research Virtual Reality centers and then watch as your morale plummets empire-wide as your Zero-G arenas are replaced.
The second is a sneaky, but devastating bug that I pointed out a few days ago with no real response so I'll post again and then let it go.
When you upgrade a ship design, the obsolete, predecessor design does not go away anywhere but on the shipyard screen. This is important, because for some odd reason and with no pattern, planets building the upgraded design will build the older version. Once this bug hits, it becomes impossible to build the upgraded design.
This bug is more serious than just the fact that you have to wade through every obsolete design on the quick build menus. This means that even if you go to the full planetary shipyard screen and select a design, you will still build the older version of the ship. This has happened to me with engine-upgraded colony ships in my last two games.
The solution for players now is simple and what I recomended in another post. Don't ever upgrade a ship design. You must simply design a new ship every time you want to change out the weapons or engines. Upgraded designs clutter the quick build menu and are also extremely bugged.