From scanning the first few WN chapters, they (MC and he D-Rank girls) are basically given put in a room that seemed to be without beds, with guards to keep them in, given only some stale bread and low end soup to eat, then given laughable gear and once the class has been broken up into groups of 4 sent to the adventurers guild to train (while everyone else is given a knight mentor). I also seemed like the princess blatantly lies about some things to keep them in line.
It also seems like they it is not a case that he hid to well, but they did not even look, The impression I got is they discarded him to E based on the class alone, since it is not a combat class, and did not even look at his abilities, when he gave himself 2 unique ones that scream "I am super useful outside battle" one being the Item Box that depending on the world is either super common or beyond broken.