It's pretty difficult to make a daily menu that meets 100% of your DRIs (Dietary Reference Intake) in a single day. I had to do it as a project in a class, and it took forever to get all the nutrients balanced! They are now called DRIs instead of Recommended Daily Allowances because you don't really need to get 100% every single day. An average over a week or so is fine - you don't need a perfect balance every day for good health. Your body will balance it out.
Though the DRIs are based on the science we know, there is still a lot we don't know. Many of the DRIs are just our best guesses as to how much is needed to prevent complications related to deficiencies. They are also set high for the average person (2 standard deviations above average) in order to include 98% of the population. It is likely that you need less than 100% of each micronutrient (sometimes much less).
Ideally, you should get as many nutrients as you can from your food. Your body absorbs them better from food (with the exception of folate). If you eat a well-balanced diet with a good variety of foods and lots of different colored fruits & vegetables, you are probably getting what your body needs. If you also take a multivitamin, then you should be in good shape. If your diet skips all of a certain kind of food or entire food groups, then you may need to take a closer look at your diet to make sure you are getting everything you need.
I hope that helps!
Edited to add: I have noticed that Fitday does not track the DRIs very well. I think this has to do with the database and possibly the way our food label information is printed. Only Vitamins A & C and Calcium and Iron are required to be listed on a food label, so if Fitday uses the food label for its information, then it could miss other micronutrients.