Today I rode 100 miles and when I look at the workout stats in Garmin Connect it reports 3,640 Active Calories + 388 resting calories = 4,028 total calories burned. This shows up the same in both the Web and iOS versions of Garmin Connect.
The Calories Burned widget is reporting 1,576 active calories + 1,416 resting = 2,992 calories burned. This is the number showing up on my watch too for today's calorie burn. Obviously, the active calories are not being passed correctly from the workout to the Calories Burned widget.
I'm seeing this happen in about 10% of my workouts (guesstimating, its roughly once per week and I do 10-12 workouts per week). Most of the time the calories burned in my running and cycling (and other) workouts are reflected in the daily calories burned in the Calories Burned widget. I cannot discern any pattern regarding why the other 10% of the time the calories are not being passed from the workout to the Calories Burned widget. I assume this is a bug.