Are you looking at the vitamins and minerals in the graph in the reports section?
The graph is not going to be accurate unless you 1) weigh and measure everything you eat, 2) only eat foods that are NOT custom foods. That's because the information on the nutrition information panel of the food does not have to be complete - the food producer includes what is required but that is all.
If you ate an orange, that information would come from the USDA database. It would have a lot of information kept by fitday in your food log.
You made a custom entry in the food log for some crumpets (I have some handy). It has calorie information, total fat, saturated fat, trans fat, cholesterol, sodium, total carbohydrate, dietary fiber, sugars, protein, vitamin A, vitamin C, calcium, and iron. When you eat a crumpet and log it, that information is all that fitday has.
If you produce a report that includes just those two items - the orange and the crumpet, the shortage of information for the crumpet will affect how accurate the report really is. There may be vitamins and minerals in the crumpet that would contribute to the report but because they are missing, you only see what information you have. Maybe some vitamin looks deficient - but maybe that has a value for the crumpet (we'll never know).
If you are only eating foods that are NOT custom foods, that's closer to representing the nutritional values in your diet in that kind of report.
This is true for any website that allows you to enter custom foods. The information is limited because your information from custom foods is limited.