Yep you're right. I was looking at when Garmin connect is synched with myfitnesspal, it seems to count both in that occasion. Would love to pause the step counter during activity for that reason.
At MFP you can activate the option for negative Calorie adjustment. It is there exactly for that prupose. Read up more about it on the website of MFP.
I'm getting double calories burnt from a run as it's adding my steps from the run.
You don't. Calories are calculated with the help of the current heart rate, average resting heart rate, and heart rate variability (assuming your device has a HRM). Steps are irrelevant in such case for the Calories calculation.
At MFP you can activate the option for negative Calorie adjustment. It is there exactly for that prupose. Read up more about it on the website of MFP.