I'm really not at all qualified to answer your questions, but I do recall reading something about a known bug with Meteor Swarm.  As for the siege ships (aptly named, btw... because that's exactly what they look like, and it's a little silly), I have also had a lot of trouble with them autousing their ability, which is their only means of offense... their weapons aren't mounted normally.  Why this is, I'm sure I have no idea, and I do think I remember talk of reworking that prior to the final release.

Obviously this was far from definitive, and I'd be interested to see what better-informed folks have to say.

Yeah, certainly possible for the starbase. The animation is a little hard to see. But I reloaded the save, just to check, and the Starfish still exhibit the same behaviour.

Thanks Annatar, I'll send it along.