I'm loving the game, it's the first one I've played with a pen and paper to write my impressions and questions in a long (long long) time. Definitely deep and meaningful mechanics. Here are a few little buggy things I've encountered during my play-through, I'll include a few pictures and I've also set aside a copy of my save file in case Stardock or anyone wants it:

1. If I have multiple ships in my queue and I use the "Commands" feature under the governance screen to update them from say "Constructor M19" to "Constructor M21" the first couple in the queue will change to "M21" but the later ones will not, so a few turns later a shipyard will once again be building "M19"s.
1. Obviously it shouldn't update every ship in the queue to "Constructor M21" because I might be building a different ship interspersed in the queue, but I would think it should search the queues and change all "Constructor M19"s to "Constructor M21"s.
2. The game is letting me build multiple "Preparedness Center"s and "Missionary Center"s on the same planet. It isn't letting me do so all the time so I haven't been able to nail down what is triggering it.
1. I've already got 2 "Preparedness Center"s on Boaz and now it's letting me build a second "Missionary Center"
2. On Oshriim you can see them already built and still both available to be built in the building options.
3. Certain galactic resources are only appearing when I zoom out to "Tactical" view and are invisible when I zoom in. See the bottom of my post for specs and I'm playing on the default "Low" visual settings (presumably low settings don't make resources disappear, that would seem bad).
1. Resources (and such) I CAN see both tactical and normal view: Asteroids, Durantium, Thulium, Promethion.
2. Resources (and such) I can see in tactical view that DISAPPEAR in normal view: Nebulas, Black Holes, Gas Clouds, Antimatter, Elerium.
1. On the bright side this has brought me and the tactical view much closer together and now I very much enjoy it.
3. Here we can see everything in tactical viewAnd here the items mentioned disappear when zoomed in
4. Not affecting game play, but planets that were in my "Influence" before I conquered them are still making a sad face at me like they're in someone else's sphere of influence (to be clear, I control them and they're in my influence). 
5. My last smaller issue fixed itself when I reloaded, but initially some starbases that had the "Assault Fighter" module were showing the green shield that they were garrisoned while some were not. On a feedback rather than bug side, I would prefer the module not make them appear garrisoned as it makes it more difficult to realize that you've got lazy constructors hanging out in starbases, although this will be less of an issue when the "Ships" list gets some TLC and is less painful to review.
1. Here we see before the save both of these have the "Assault Fighter" module already built (it is not being built this turn for either of them) 
2. Here we see it after I saved/loaded and this issue appears to have fixed itself 

Tech specs:

• i5 2500k @3.3GHz
• GTX 570
• 8 gigs of RAM
• 7200 RPM HDD