Fun game.
Glad you're enjoying it!
Sometimes my ships attack the AI command station when I only give an "x" move command near the station. This is annoying if I haven't saved recently. Is this a bug or does the command station occupy a "physical" space larger than its image?
Yes, the command station (like many ships) has a space larger than its image. You can hold down I think the A key... or something like that, to see the total space. The ring is the area in which you will click that unit.
My transports are not unloading my ships. I keep having to let the AI destroy them to get my scouts out which defeats the purpose. I have read and reread the transport dialogue box but there is nothing telling me about limits except the 10 ships per second rule. My transport is not being fired upon and is not moving. I left click on the unload button and get nuthin'. Is this a bug?
Note the text that says you can't unload when too far away from the planet -- most likely that's what is going on, is that you're too far away from the planet's center and thus it won't let you unload. I think a message shows up in the tooltip when this is the case.
My scouts show up on enemy planets with a blue number. My scout star ships do not show up as a number. Definite bug.
It probably has to do with how the scout starships are categorized. If you change it to show all your ships rather than just mobile military ships in the filter on the galaxy map, that would fix that. But yeah, it would be better if they also qualified as mobile military ships.