Ultrathin manganite films have been investigated by Scanning Tunneling Microscopy down to surface atomic resolution. Previously unknown surface features, consisting of small non-stoichiometric islands have been revealed. On this basis a conceptually new mechanism is proposed for the growth of these complex materials, widely used as active electrodes in organic spintronic and other devices. The observed non-stoichiometric islands result from nucleation centres, whose size does not reach a given critical threshold value and represents eventually an intermediate step in the single layer growth. We claim such defects to be characteristic for all the thicknesses, representing thus an important parameter to be taken into account in various applications.