I've noticed a few strange things, like construction frigates that start construction and then stop. It's really strange, sometimes I've about 8 buildings that are half finished. After a while (can be 10 minutes or so) construction resumes, but it takes a really long time to finish construction this way.
And there was this Orkulus Starbase that moves to attack position and then ... well it doesn't attack. It seems like it stopped just outside attack range. When I gave it an explicit attack order it did attack... this happened at least twice, once against a siege frigate and once against an enemy starbase that was being constructed. It happened while I was looking elsewhere (I wasn't focusing on the gravity well) and I only noticed it a lot later when I actually zoomed in on the gravity well.
Also, at one time I've noticed how an Orkulus starbase pushed away a Titan from a planet bombardment and the Titan didn't move back into bombing range. It was only after I ordered it to attack the planet again that it moved back into its bombing position.
This leads me to think, maybe these things have to do with the range checking ... maybe the ships thinks it's in range, but the weapons or construction beams think otherwise ...
Also, on several occasions I ordered an Orkulus starbase to move into a region which contained a set of defensive structures, so that it would stay close to the repair bays. When I looked a while later (I noticed an enemy fleet coming in) I saw that it was still trying to move in position, but it couldn't because there was no room. It was stuck there and completely ignored the fleet. It was only after I pressed "S" (stop) that it turned around and started attacking the invaders. I think it's strange that the ship just keeps trying to move to a position that it can never reach...