The FitBit is an accelerometer, which means it measures acceleration and that means it does its thing best when you are moving forward. This is great if you're into running, less so if you're on a spin bike. FitBit uses algorithms to approximate calories burned based on your movement, and they do a pretty solid job of using feedback data to update their algorithms, but since it is not a heart rate monitor, it isn't very accurate at calculating calories burned from other forms of exercise.
This leads me to stand behind my statement that FitBit hates on CrossFit.
Let's take a look at what FitBit calls Very Active Minutes. FitBit's Help site says,
"You earn 'very active minutes' when you wear your Fitbit while doing cardio workouts and high-intensity activities like jogging and running. Note that your active minute count will be lower for activities that are not primarily step-based, such as weight lifting, cycling, and rowing."
I'm pretty sure CrossFit is the definition of high-intensity activity.
Now let's take a look at my FitBit dashboard for April 15, 2014. I had 3 Very Active Minutes and you know what the WOD was? ONE HUNDRED FRICKIN BURPEES FOR TIME. It took me over 10 minutes. Where are my other seven very active minutes?!
It doesn't matter how hard you work or what barriers you break - if there is no running in the WOD, be prepared to be told that you lay prostrate on the floor eating macaroons all afternoon. You can override the thing and input your own exercise but there's no CrossFit option. The generally accepted substitute on MyFitnessPal is Circuit Training but I don't bother to change it. Normally I'd advise you to wear your HRM to get an idea of calories burned during a certain activity but since no day at CrossFit is exactly alike, that's not going to provide you an accurate number.
My best advice is to remember that the FitBit is not supposed to provide you with an accurate number of calories burned but should rather be used as a motivational tool. It's really hard to justify taking the elevator when it's midday and you're only on your second light.