Why did the inverse correlation of stocks and commodities stopped working in 2008? Usually, the commodities asset class is considered being inversely correlated with other asset classes, due to its nature of an input for manufacturing (if the prices of commodities go down, the manufacturers can produce for less, and have a larger profit, and vice versa). 

Therefore, why during the stock market crash of 2008, the commodities also went down, by far? What happened macro-economically to stop this inverse correlation from working?
The problem in your question is the "and vice versa".

To give a very simplistic view, the problem in the 2008 crisis was not on production side - companies had enough to produce, but no-one to sell to. Given this, excess commodities found no buyers, even as the price lowers. The inverse correlation of stocks and commodities supposes full capital use, which is not the case during the 2008 crisis.

Globally, the correlation between commodities and other stocks is around 0, though during full capital use periods it does tend to be negative, there is usually a positive correlation during crisis.