I thought it happened to me once, but i'm still not sure about that. If it happened, problem was that i haven't got enough storage space, but was about 200 units short, and because of that i failed to receive 2500 of the same unit, leaving me 2300 short, because i assumed i'll have space enough, and even if i don't, it'll fill the remaining space, which didn't quite happen. Again i'm not sure about numbers and if that actually happened, so there might be another explanation.
The thing is that it doesn't refresh immediately, and to refresh, the best way is to either demand from villages, or to put resources into market, or to try spending some resources. After that you can get the report of trade if it didn't show up, and true amount of resources you have. Also, even if it doesn't show the right resources, you'll still be able to build buildings (troops) that require more resources than it shows you have, but less or equal than the actual amount.