Just bought the game yesterday (because it doesn't use any copy protection, specifically starforce, which I hate with a passion) and I've already encountered an irritating little bug.
I'm not exactly sure how to recreate it but I'm sure it had something to do with taking ships out of autopilot and giving them a new destination. Every so often I get the orange ETA text stuck on planets even when there are no ships heading there, at one point I had an entire disbanded fleet (8 or so ships) leave their 8 seperate eta's on the planet when they landed.

It seems to go away after a load game but it's still rather annoying.

P.S. Is there any way to upgrade ships in a fleet without breaking them apart into seperate tiles and selecting them individually?