Confusion on daily food journal/exercise

It's because when you add your exercise, it credits (debits?) the calories burned into your daily allotment. I don't put all of my workouts and calories burned into my diary for just this reason. I don't want to mistakenly devour my deficit!
Hope this helps!

MFP works on the NEAT (non exercise activity Thermogenesis) system of calorie counting.

This means your deficit is built into your basic calories and you are supposed to log and eat back* your exercise calories to maintain the nutrient and energy levels to sustain the exercise you are performing without your daily activities suffering.

*MFP and most gym machines overestimate calories burnt. It is best to start by eating back 50-75% initially,and adjusting the number up or down so you are losing at the rate you specified when you entered your stats into MFP.

What use is it doing an hour cardio/ weights when you are too tired to get off the couch the rest of the day?

Cheers, h.

NB: if you derived your caloric needs through an on line TDEE estimator, your calories from exercise will have been included in your calorie goal.

I exercise specifically so that I can eat more I'll usually leave myself a buffer of about 100 calories to make up for inaccuracies in counting and exercise estimates, rather than calculating a percent to eat back.

If you are eating at a large deficit already (e.g. you're down at 1200 calories/day) and you don't eat back your exercise calories, you can actually make yourself sick - bad skin and fingernails, losing hair, etc. I've never done that, but I do know that if I don't eat something after a high-burn exercise session, I am pretty wiped the next day.