Firstly, you cannot simply be "missing" the shoes. Either they're in an obscure inventory or you threw them out.

More importantly though, you don't want to be putting them in the dresser anyway because paid outfits can be put in the armoire and it's a better deal all round. (I'm not sure why they even bothered adding the outfit option for them.) It doesn't cost prisms, doesn't take up any dresser slots, and – most relevant for you right now – they are inserted as individual pieces so it doesn't matter that you don't have the shoes.