I've also noticed that the numbers on nutrition panels often don't add up. I think they often are just inaccurate.
But there are food items that have no fat, protein, or carbs yet they have energy value. consider alcoholic spirits - while the alcohol is a carbohydrate in the chemical sense its not a sugar / starch in the way carbs are defined in food circles. So rum has 212 cals per 100g yet will be listed as having zero fat, protein and carb.
Maybe your example has a lot of compounds that have energy value but no nutritional value like the rum. Sorry but I have no idea what they could be in your case.