Provided that you measure food correctly (using a working food scale) and that you use information in some kind of coherent way (to test if you're over or under-estimating) then you can be sure that calorie trackers would not "lie" to you in a non-negligible factor (±8%) which would gut burnt over by your daily activity, anyway.
And real science, in reality, supports that for most of the time (i.e: you're neither super-obese nor an olympic athlete) a calorie is a calorie. See: http://www.bodyrecomposition.com/fat-loss/is-a-calorie-a-cal...