Instead of your production reducing the buyout cost of a ship or tile, when you buy out a ship or tile you just pay all the cost and waste all remaining production for that turn.  It doesn't get stockpiled for the next turn of construction.

Oddly enough it is also slightly different for ships as it is for tiles.  With tile buyouts you pay the remaining manufacturing cost of the tile.  With ships you always pay the full manufacturing cost of the ship, even if it is 99% complete.

I would propose that either your manufacturing should directly reduce the remaining buyout cost of a ship or tile, or at the very least that production should be stockpiled for future items.  And ships should not cost the full amount regardless of production progress, that's just silly.