I haven't played in a while, but this sounds familiar...
If I understand correctly, GalCiv isn't giving you an error, it's not just doing anything after you press the turn button.
If that's the case, it's most likely the result of a ship that's waiting for an order from you. Pressing the Tab key will take you to the ship that's wiating for your order and pressing the Space Bar will skip that ship and proceed with the turn. Keep in mind, it's possible to have hundreds of ships waiting in such fashion so you may have to Tab/Space Bar more than once.
There's also an option in one of the menus regarding auto-pilot ships and skipping them at the end of a turn that you may want to check out.