Well, I haven't checked if these issues have already been reported here and I'm not sure if these are really bugs:
In my advanced game I researched the final farm technology (advanced farming) but noticed that it yielded no bonus at all to any of my farms. After upgrading them, they keep to the value they had before (8 mp).
I think this is a bug as there seems to be no benefit from this technological advance.
Another issue which I suppose is a bug concerns the sudden lost of effect for influence starbases. In my game the Torians defeated a minor race possessing a few colonies. I have built a net of influence starbase around these planets. The starbases are upgraded to the latest possible influence module. Anyway shortly after the Torians conquered the few planets all of my starbaces totally lost their effect. I noticed that building new influence starbases would only have a local effect which would not extend to the already existing ones.
Finally I experience sometimes random crashes to desktop. I do not think that they are related to my system as according to the windows event viewer they are caused by access violations.
My sys specs:
Win XP SP2
P IV 3.0 GHz hyperthreading
2048 MB RAM (the game seems to be very memory consuming)
ati 700 se (latest ati drivers installed)