stored goods go up every time you build something and have leftover production. it goes down every time it would take more than you make in one turn. i could see a bug like this getting caused by the AI using money to rush stuff every turn and not using the normal construction method. if the numbers were lower, maybe building a ton of cheap buildings to build it up would make sense. I do this myself building space elevators and factories, then after i get a bunch of stored goods spending it on a multi turn building like a colony capital upgrade or terraforming
shipyards work the same way.
a screen shot that shows your turn number could help. err nvm, this game uses stardates and stuff. sorry i play so many games that just use a simple turn #. started game up, if you mouse over the star date it shows your #
Assuming you didn't use any mods or custom factions, your save might help. but we would need the same dlcs as well. on my end i think i have them all, but might need to double check if i am missing any.