When logging an activity that involves making actual physical "steps" (running, walking, jogging, hiking, backpacking, golf). MyNetDiary will automatically estimate the number of steps you have made during that particular exercise and subtract them from your overall Step Bonus amount.
This functionality is in place to avoid logging your burned calories twice (first as a logged exercise and second as a step bonus), thus preserving the correctness of your diet tracking.
Please note that the app will calculate and subtract duplicate steps only when the exercise in question has miles-per-hour (mph) or kilometres (km) indicated as one of the "amount" options.