Long standing issue is that it 'gave' you exercise calories without netting off those already in your daily allowance. So depending on your size/BMR and which activity bracket you chose, it could be anywhere between 10-30% too high.
I input running and walking calories that I've collected from Runkeeper, which also gives you number of calories. And up until a few days ago, the number on both was pretty much the same.
But now MFP seems a fair bit lower. Have they finally netted it off? Because if so, I'll start eating all my exercise calories, not just 2/3 of them!