Hi Ironsides, thanks for the bug reports, the images and the save files. They were invaluable to determine the source of the issues.
These were quite specific bugs, which were well hidden till now. Let's go one by one.
There was an issue when spy leaders couldn't fulfill their missions (e.g. Dexana couldn't influence any leader on the Moltar, in your case) which would cause them to lose opinion immediately in the next turn, when in fact they simply couldn't fulfill their mission. Dexana sees a -2 drop in opinion because she has the Fickle trait, where leaders lose opinion more rapidly when unassigned.
This is resolved, and spy leaders will only see their opinion drop 5 turns after they become unassigned after they end their spy services, like the other regular leaders do. A fix will be available in the next update.
This one was very hard to reproduce and very specific. This issue only manifested when you captured ships that were assigned to invade an outpost belonging to a 3rd party on that system. So, what happened is that the Sulak ships were ordered to capture that Palacean outpost. After you captured the ships, you then took the Sulak outpost. However, the game still allowed the captured ships to fulfill their original assignment. So, they invaded the Palacean outpost, resulting in your empire invertedly declaring war on the Palacean, since they now belong to you Quite nasty this one.
The good news is that this is now resolved and a fix will also be available in the next update.
This one has two components. The main issue is that your Planet Construction project didn't finish in the turn it was supposed to, due to a wrongly reported ETA. This happened because the colony base project was rushed, resulting in the ETA precision error for the Planet Construction project (the calculation was correct, but the reported value was not). This is now resolved. The planet construction will finish in the next turn now, and you'd be able to build the colony base on it. A fix will be available in the next update.
The other component is if the colony base should be allowed to be cancelled or not, when it is finished and ready to be deployed. There's already an item on the big list to consider looking at this, when the opportunity arises. So, we'll see.
Thanks again for reporting these issues.