Clicking on a stockpile gives me wildly inaccurate numbers for what's stocked there. It says I have 115 planks, when I have 10. 15 hematite when I have 3. 5 coal when I have 0. The colony stocks tab seems to work okay, and the tooltips on the stockpile icons tell me what I actually own but... the at-a-glance functionality is nil.
Guess I should have done that first, huh? The large stockpile near the graveyards is what gives me trouble, I don't usually mess with the small food-only ones.
Bump because I think I've found the cause. "Accident" type events that destroy items without using them for a task seems to not subtract the destroyed items from the stockpile tally. Selenians ate 1000 prepared meals, but my stockpile still shows them. I had a fight ignite gunpowder in my stockpile, which blew most of the stuff on there to pieces (don't be me, kids!). It didn't register the destruction of some stuff but not others. Hopefully that's a place to start.
