Not something wrong with the game, no. Some products will be in flux, others will more or less always be in the red. In the red is good for you, it means that those items are in high demand and you can make a profit if you produce those items.
Most natural resources tend to be in the high negatives and are the most profitable, but will eventually run out.
To avoid some serious shortages, like factory and asset maintenance, I have my Country buy those either from contracts in my Common Market or my Enterprise.