This is due to a couple of reasons:
Food manufacturers are allowed to round up or down by 5 calories so if something has 2 carbs for example which totals 8 calories, they package may only say 5 calories.
Food manufacturers do not have to claim the 4 calories from a fiber carb as calories in the food, since there is debate over how many calories from fiber are actually absorbed by the body. But the total carbs contains the carbs from fiber in your nutrition facts. Unless you put in Net Carbs, which I do not recommend. Just count them. It may help you lose weight faster if you’re getting a lot of fiber carbs!
Sometimes users add foods to the MFP database and only add the calories but not the macros, so check what you’re adding to your diary!
Math from each food item entered may not add up exactly due to rounding from some items when everything is totaled.
BOTTOM LINE: Worry about your macros and not your calories!