Of course it's possible if you're eating 3000 and burning say, 4500. The "all calories are not created equal" has more to do with how various foods affect you metabolically, and how they will thereby influence body composition.
FOr instance, 2 cups of broccoli (food A) has x number of calories but has virtually no insulin response to eating it and takes 2y calories to digest. A slice of light wheat toast (food B) has x calories too, but takes y calories to digest an ilicits a large insulin response. Therefore x calories from broccoli is the better option if you are trying to lose weight body fat when choosing between x number of calories from food A and x number of calories from food B.