Exercise tracking with Apple Watch or Map My Fitness

I depends on how the Apple is synced/linked.

If Apple watch is merely being used as a step source, then MFP is going to very roughly estimate how many of those are already in your selected MFP Activity level, and any extra steps roughly estimate how many extra calories you burned above that level.
Perfect sense. Very rough, but good in theory.

You do more you than initial estimate (activity level), you eat more.
You do less then you should eat less too - hence the MFP option to enable Negative Adjustments.

MMF workout entry will sync over with a time stamp IIRC and they haven't changed anything.
But there is no time record for the steps and calories used, so MFP has no idea if the steps were part of the workout or not - so to avoid potentially double counting, the workout entry calories will actually be removed from the extra calories.
If it was a walk then fine, part of the steps was part of the workout.
If it was the bike ride (or other non-step activity), then steps are not actually.
But the calories in the workout will be removed no matter.

So if you had a very active busy day, well above say Sedentary and burned extra 300 by rough estimate of steps, and then you burned 250 more in a bike ride with no steps that MMF synced over, you'd end up with only 50 extra (+300-250), when it easily could have been 550 above and beyond sedentary.

So actually eating less when you do more - wrong way to power your workouts and aid recovery frankly, make that a consistent thing increasing your deficit beyond reasonable and could stress the body too.

If the Apple watch is linked right, and you made a workout on Apple's system, that workout also synced over.
That should have a time stamp on it, likely matching the one from MMF, so there won't be double addition/subtraction.

Edit each workout entry and see if there is a time there, then cancel out.
Enable option for Negative adjustment.
On the line about Adjustment, tap and hold for more details.
Screen pic and share that detailed screen if you want clarification as to what your setup appears to be.