Not sure if this is a bug or by design. The resource amounts only includes what is in building storages. I think it should also add in any piles left on the ground to accurately reflect what you have. For example, when they cut down a tree the logs are left there; they’re just as good as the ones in storage.
Also, I think the count should also include what’s in transit from one storage location to another. It’s odd that resources disappear when a laborer or wagon takes them out of storage and magically reappear when they are dropped off. If the destination is someplace where the resource will be consumed, like food for a shelter, something needed for production in a factory, or materials for a build site, then it makes sense for the resource to be considered used up when it is taken out of storage.