I think I've seen this before. What is happening might not be what you think. I think there is the possibility where you don't rush buy to finish a ship, but instead you rush buy to buy a new ship.

Hmm... I was thinking that was no difference between Terrans and Alterians. I'll test the Alterians later then.

I did some intense testing, and I found a serious bug that would all me to rush buy ships for free. I even went so far as to start a new game to test things out. Every ship I tried to get for free, I've got for free. I was the Terrans when this happened.

I've already figured out the free ship bug. Thoroughly. I'm still working out how to explain it. I should be able to post it shortly.

Back on topic, I tried to play as the Altarians, but their shipyard stuff hasn't played out differently than what it did as the Terrans. There is a circumstance where the shipyard will display the wrong numbers, but the actual amount taken from the treasury is the correct number. Correct number being the number that takes into account how much work has already been done.