Outstanding crystalline perfection is a key requirement for the formation of new forms of electronic order in a vast number of widely different materials. Whereas excellent sample quality represents a standard claim in the literature, there are, quite generally, no reliable microscopic probes to establish the nature and concentration of lattice defects such as voids, dislocations and different species of point defects on the level relevant to the length and energy scales inherent to these new forms of order. Here we report an experimental study of the archetypical skyrmion-lattice compound MnSi, where we relate the characteristic types of point defects and their concentration to the magnetic properties by combining different types of positron spectroscopy with ab-initio calculations and bulk measurements. We find that Mn antisite disorder broadens the magnetic phase transitions and lowers their critical temperatures, whereas the skyrmion lattice phase forms for all samples studied underlining the robustness of this topologically non-trivial state. Taken together, this demonstrates the unprecedented sensitivity of positron spectroscopy in studies of new forms of electronic order.