I mentioned this in another thread:
When you're running the game in windowed mode, if you're still holding down the left mouse button and accidentally go off the GalCiv2 window, when you come back it'll assume the mouse button is still held down, even if you let go of the button before returning the mouse to the screen. Not sure if it's fixable, but it's annoying. When you're just trying to drag the main map or the tech tree up or down a bit, you have to be *really* careful not to go off the screen or else you'll wind up going all over the place.