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It drove me crazy trying to track down, among my 250 active mods, which one was suppressing the new features for marking items by “Unwanted” and “Unusable in Recipes”. Turned out it was this mod (the version before the Sep 28 @ 2:28am update), specifically the “EatSmartInt” submod.
After the update it works properly. You should really make it clearer that subscribers need to re-subscribe to get the new menu options and avoid conflicts with other mods.
Keep in mind that some foods do not reduce their weight when partially consumed, although they do reduce their total amount of hunger, calories, fat, etc.
I'd need more context to better address your issue. Is it happening with a specific type of food? Was the food you ate in your inventory or in another container? Maybe you're using a mod that could be affecting it, and it would be good to find out which one is.