I'm personally working on a game content update - in fact I finished it last night - that *should* correct problems like this.
The standard game database is full of errors like this, such as buildings that aren't set to upgrade properly, buildings that have no construction costs, buildings that have the wrong bonuses set, missing minor races, minor races whose species has been set as Human, etc etc. Chances are you've got two shipyards because they aren't upgrading correctly or haven't been set to be mutually exclusive of each other.
The problems are the result of several different people in that past working on the game at the same time, and using different versions of the "final" game reference database to make those changes. Since different people were making different changes, a lot of things inevitably got overlooked. Chances are some problems will have slipped through the net even in my own update because the final version of the game reference database has been updated even whilst I was performing that update, but those *should* be few and far between. You can find the current version of the reference database
Here.I've sent the update to Mike (The developer), so it is just a matter of time now before he makes it available for general release. People will then be able to notify me if they notice any problems so I can fix them. The next update that I will work on will focus on the shiplist, because many of the ships are missing or have inaccurate stats.
_________________"Anyone without a sense of humour is truly at the mercy of the rest of us."