I am currently experimenting using the Apple Watch and FitBit Charge HR with MyFitnessPal.

I was seeing a difference in steps taken on the MyFitnessPal app versus steps used and converted as extra calories for the day when using the Apple Watch. The FitBit Charge HR doesn’t have any problems.

So I emailed MyFitnessPal support and below is the response received.

Thank you for taking the time to contact us. We’re sorry for any inconvenience you’ve come across. When you connect your Apple Watch, the steps are recorded throughout the day on your homepage as you have observed. When our program updates your adjustment in your diary, we pull the data from your Homepage periodically. Therefore, as your steps increase over time, the steps in your diary will not reflect that unless they are updated. We are definitely working to improve this aspect of the program and appreciate your understanding.