I find Galactic Civ 3 is generally pretty good at keeping track of production overflow. However, I've noticed that when I choose military subsidies in the social manufacturing queue, then the existing accrued production overflow isn't sent to the shipyard, it is simply lost. This can result in the loss of a large amount of production as I tend to play with social manufacturing set to 100% and rely on military subsidies to build ships. I am playing the opt in 1.7 update.
Can anyone else confirm this bug?