FYI: MyFitnessPal will not go below hard coded minimum calorie recommendations, I would guess for liability reasons. 1200 for women, 1500 for men off the top of my head. If you set your profile as sedentary, then add exercise calories after (as is the best way in my view) this could very well be above the true 500/750/… calorie deficit you wanted the app to set.
To work around this, you should set your baseline calorie goal manually.
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