I had the same issue, while playing TEC, when building from a starbase with lvl 1 construction. It wouldn't deduct from supply until after the ship was built, and would let me queque up ships WELL beyond the available supply. It would also let me build 1 ship beyond was was available (supply would go into negative, and it wouldn't build any further, even though they were still in queque)
This only effected the one starbase, not others that were developed to lvl2, nor did it effect any frigate factories