I haven't heard or read anything about inaccuracies. If you really question a food's caloric value or other values, you can make a custom food that you have from another source and use that instead. But everything I've ever counted has been right in the ballpark of what I imagine it would be and there have been no surprises there.
The real inaccuracies come when you count, measure, weigh the food you put in your mouth! And conveniently forget things! Like butter or sauces, or even beverages.