Are there any calories in roasted coffee beans? Why is black coffee 0 kcal?
Flatly, the calories are in the filter: in the grounds that you dump on your compost.

In the water that went through the grounds, there are mostly aromatic substances and traces of coffee oils, few enough that a cup of coffee has (rounded) 0 calories.

The caloric values given for coffee beans are valid if eaten - which is rarely done in significant amounts (except perhaps the occasional chocolate-covered bean or truffle garnish). That the values differ between sources is typical - it happens with other foods as well. Measurement methods vary and so do nutrition contents in different batches / breeds / origins of beans. 

If you prepare your coffee with a method that leaves some coffee grounds in your cup (e.g. Turkish coffee) and you consume them (as opposed to leaving the dregs), your cup will have some calories. Yet probably not enough to be relevant for your daily calorie intake. My estimate would be that an amount of black coffee that would supply a significant amount of calories would have you shaking that much that you would burn them again just from the side-effects of the caffeine or from the additional trips to the bathroom.