In the first place, yes you would subtract calories expended while working out when determining you calorie defecits. Your trainer appears to be shooting for a daily defecit of around 500 calories (eating 100
fewer calories than you burn plus the 400 or so you burn working out) which would ideally result in a loss of one pound of fat per week (there are ~3,500 calories in one pound of fat).
The thing is, as MostMuscle has pointed out, you have to remember that these estimates are all exactly that: estimates.
Other things to keep in mind?
You say you're careful about what you eat. Does that mean you measure and log everything? Strict logging isn't exactly necessary but it can be really helpful and if you're not doing it you should give it some thought.
Also, forget about targetting your heart rate to any so-called '
fat burning zone'. While the whole 'work less hard and burn more fat' thing looks good on paper it doesn't really withstand closer scrutiny and you're really just cheating yourself by not working out harder during those cardio sessions.
And yeah, don't get too caught up in scale readings. Scale weight can be a half-useful measuring stick but it doesn't account for fluctuations in water weight or changes in body composition. There's nothing wrong with keeping an eye on your weight but also pay attention to other indicators like how your clothes seem to fit and how you look/feel.