when net calories are in the negative??

Hate to be Debbie Downer but negative means you ate more calories that your defined goal allows. Do some cardio to compensate!

It's not a stupid question at all. It means that you've burned more calories (exercise) than you've taken in thru food. It's not a good thing to see at the end of your day. If you workout first thing in the morning like I do it's common but as soon as you eat it should disappear. Your gross calories is all the food you've eaten. Your net calories is all that food minus your exercise. Most people eat back their exercise calories (sensitive topic on here) so that their net calories reflects the amount of calories MFP told them to eat for the day. Or at least close to it.

You don't want your body in starvation mode because it will hold onto the fat even harder. (Been there)

You will need to fiddle with eating back vs not until you find what works best for your body. Listen to your body, it will tell you what it needs. Don't worry, it takes time to be able to hear what it's saying. Lots of advice on here to help you along the way.

Hate to be Debbie Downer but negative means you ate more calories that your defined goal allows. Do some cardio to compensate!

Not true, sounds like you are getting confused with the green "under by ... calories" in your diary compared to the red "over calorie goal" which shows as minus .... calories

Negative NET calories means you are consuming less calories than you are burning through your workouts. For example, you eat 1500 calories but burn 2000 through a workout, you are then at -500 for the day
This is exactly the same as not eating anything and then having a 500 calorie burning workout. Alright for 1 day, if say, you run a marathon, or spend the day hiking, or another one off event and physically can't eat all the calories you burn. Apart from that you should be at 1200 net at least.

Its not a silly question and can be a bit confusing, I will try my best to explain it without confusing you further. (you can see what i'm describing under home>goals, and food logging screens) When you give your information to my fitness pal it calucates out about how much energy your body needs per day (energy burned from daily activity on the right column) then you select how much weight you want to lose each week this amount shows as daily calorie deficit. On the food screen at the bottom you will see a row that says goals that is the daily activity amount minus your deficit amount IE 2520-490=2030 the remaining is in the example is your goal amount minus the total of all the food you've taken in so if you are in the negitive until that negitive number is GREATER than your deficit amount you were still in maintence. In the example 2030 is my goal if I ate 2520 the remaining will show -490 (this equals but is not greater than my deficit amount which means I mainatained my weight and didn't not gain nor lose anything.
Further if you enter exercize this adds to the goal amount that you can eat, basically its all laid out so that however much you eat or exercize you end up with the same amount of loss everyday. I hope that makes sense and is helpful. Have a great day and God Bless.