Too many calories ????

Keep in mind that most exercise calorie calculations give gross burn - including heart rate monitors. Gross figures are only useful if you assess your entire day that way, hour by hour, and then add them up. If you take a base burn figure for your day, and then add exercise on top, you must use net burn figures otherwise you effectively double up on your base burn during that time - i.e. the calories you would have burned were you to just sit on your backside and pick your nose instead of going for that run.

For short exercise sessions, it's mostly negligible, and you can still make progress ignoring it. But the longer your workout, and the heavier you are, the bigger the impact.

Example -
For a 160 pound person running 10 miles, gross burn = 1,200, net burn = 1,000, difference = 200 Calories.
For a 250 pound person running 10 miles, gross burn = 1,875, net burn = 1,575, difference = 300 Calories.

The solution is to either consider net calories for workouts, or to everything via 'base burn' only, and don't log any exercise. i.e. shift from sedentary to lightly active, or lightly active to moderately active, and allow that to account for your workouts.