Have I discovered the reason why some may not lose as quickly as they think they should?

Today when I was running and calculating/approximating how many calories I burned, it hit me - shouldn't I deduct the calories I'd burn ANYWAYS from the grand total?
For example, run 5.3 miles in an hour = 477- 530 calories burned.
But if I just sat for that hour, with my BMR I'd burn 60 calories anyways. So shouldn't one subtract the calories they'd burn anyways with their BMR from their grand calories burnt total?

Calorie count does this automatically for you when you enter an activity in your activity log.

It might be one of the reasons; I can see many people just searching for an activity and adding up the numbers to their BMR without actually logging it. Might have even done it myself a few times.

But the more common reasons for stalled weight loss are eating too much or too little, either knowingly or by accident (overestimating or underestimating portions).

Yes. If you are trying to lose weight it is important to remember that you would have burned a certain amount of calories just being alive. Although this makes all our hard work seem lessened, it does make us realize that maybe we didn't burn as many calories as we thought.

I agree...

Yes. I don't use the CC tools to log my calories, I use a HR monitor, but I know that I burn a little over 100 calories an hour naturally so I deduct 100 from my grand total for every hour I go.