We have to say that we can perceive the 'in' because otherwise we could not know whether the cup had coffee in it. And we have to say that the 'in' is real because if it wasn’t how could we drink our coffee? So what has gone wrong?
Another question arises with the concept of a structure. Protons and neutrons are structures of quarks, atomic nuclei are structures of protons and neutrons, atoms are structures of nuclei and electrons, molecules are structures of atoms, single-celled organisms are structures of molecules, multi-celled organisms are structures of single-celled organisms, species are structures of single-celled organisms, habitats are structures of species, and the biosphere is a structure of habitats. At each level of these structures novel properties emerge, such as life, organs, brains, and mind. This pyramid of structures is here called the Grand Structure. It is important in philosophy of science because every branch of science is concerned with some part of it: it is the focus of all the sciences. But what is a structure? Can you define it?
Read this book for answers to these questions, and much more fascinating stuff about relations.