The following are several bugs i've noticed in my latest game.  My apologies if they are already known.

1.  The Advent's ability to generate culture automatically on their planets (via tech research) does not go away if the planet is bombarded.  Meaning it's possible (moreover, i had this happen) that you can run through their entire territory destroying every planet and not be able to colonize a single one because they are all still generating enemy culture.

2.  The nanite swarms created by the Rankulas can be fleeted. (Bug or by design?)

3.  The nanite swarms created by the Rankulas can phase jump if selected and ordered to.  (Bug or by design?)

4.  The nanite swarms created by the Ranulas have the wrong ship icons.

5.  If an artifact is located on an asteroid and the asteroid is stripped to the core, the result is an uncolonizable asteroid belt WITH a remaining artifact that you can not access. 

6.  Spawning a phase stabilizer from a Vorastra titan in a gravity well that already has one and then decomissioning one of the phase gates will result on the loss of phase stablization in the gravity well; even though one of the phase stabilizers still exists, requiring you to decomission the second one and to rebuilt it.  (found this out by pressing the wrong ability button in a big battle.)

7.  The Jarrasul's Drain Planet animation is not properly aligned for the new dwarf planets.

8.  Zooming in on the Kostura cannon can sometimes result in it's loop audio looping at full volume indefinately even when zoomed out.

9.  Stripping an asteroid to the core leaves the crystal and metal resources in it's gravity well unatainable.