Well, the message always happen, and at the end we just don’t use any stuff at ground - i mean we can USE them but they don’t disapear.
Any stuff you use in a craft, while being in your inventory, is used & disapear like usual but with the red message.
Also, we always were able to craft stuff from rotten food, but it end with rotten tag if one of the component have it too.
After the bug with the fresh rotten is gone, feel free to report if you find again some specific craft that don’t produce rotten food while using rotten one (just don’t forget that some food can’t rot but can be crafted from rotten stuff)