Fitbit sends over a calorie burn that is mostly just bmr calories first thing in the morning since you have been sleeping.

MFP's math is done in a way that it predicts you will burn a set number of calories every hour.

So I'll use me as an example:
MFP estimates 1800 to maintain or 75 calories per hour/1.25 calories per min
Fitbit gives me 13 calories every 15 mins to account for my body's bmr.

So lets say it's 6 am. Fitbit will send a calorie burn of 312 to MFP at around 6 am, because I've been sleeping.

MFP looks at that and says, well there is still 18 hrs left in the day. If I assume that she is going to at least get to the activity level she selected for the last 18 hrs of the day (18 x 75 =1350) then add to what Fitbit has already sent over (1350 + 312 = 1672) she isn't going to burn the 1800 calories I predicted. To maintain her deficit, I'm going to need to take away 128 calories.

The math will be recalculated each time you sync your fitbit, because of the way it's done though, it's not unusual to see a negative first thing in the morning.