In this paper, we address a number of outstanding issues concerning the nature and the role of magnetic inhomogenities in the iron chalcogenide system FeTe1-xSex and their correlation with superconductivity in this system. We report morphology of superconducting single crystals of FeTe0.65Se0.35 studied with transmission electron microscopy, high angle annular dark field scanning transmission electron microscopy and their magnetic and superconducting properties characterized with magnetization, specific heat and magnetic resonance spectroscopy. Our data demonstrate a presence of nanometre scale hexagonal regions coexisting with tetragonal host lattice, a chemical disorder demonstrating non homogeneous distribution of host atoms in the crystal lattice, as well as hundreds-of-nanometres-long iron-deficient bands. From magnetic data and ferromagnetic resonance temperature dependence, we attribute magnetic phases in Fe-Te-Se to Fe3O4 inclusions and to hexagonal symmetry nanometre scale regions with structure of Fe7Se8 type. Our results suggest that nonhomogeneous distribution of host atoms might be an intrinsic feature of superconducting Fe-Te-Se chalcogenides and we find a surprising correlation indicating that faster grown crystal of inferior crystallographic properties is a better superconductor.