Boy this can get complicated @TamLivvy
Lets look at a few things,
The body burns calories when laying in bed, this is called your BMR.
The two sites calculate calories with different math. Neither is perfect, both are based on general guidlines, unfortunately their is no such thing as a general person. We are all unique and burn calories differently. Two people, same age, weight, height can walk together and each burn a different amount of calories.
Most people that have connected these accounts use MFP to log food and use their suggestions.
If your last sync of the tracker was more than 15 minutes ago these numbers might be off.
When it comes to Fitbit the user has set up a calorie deficit for the day. If at this point of the day your out calories minus your in calories are over the deficit your considered over.
Im not sure how MFP does things, but since you have your accounts linked i would go by what MFP says.
It also is a good idea to use comon sense when planning menus.
As for following the recommendation to the letter, this can lead to failure or possibly gaining weight, because the user is using fitbit as a license to eat. This has been documented, why im gaining weight with my tracker , The fitbit mistake.
The key to losing weight is to relax the mind and use common sense.
The formula is really simple increase activity and eat less, but where does the weight go
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