Hybrid samples combining superconductors with magnetic topological insulators are a promising platform for exploring exotic new transport physics. We examine a Josephson junction of such a system based on the dilute magnetic topological insulator (Hg,Mn)Te and the type II superconductor MoRe. In the zero and very low field limits, to the best of our knowledge, the device shows, for the first time, an induced supercurrent through a magnetically doped semiconductor, in this case, a topological insulator. At higher fields, a rich and hysteretic magnetoresistance is revealed. Careful analysis shows that the explanation of this behavior can be found in magnetic flux focusing stemming from the Meissner effect in the superconductor, without invoking any role of proximity-induced superconductivity. The phenomena is important because it will ubiquitously coexist with any exotic new physics that may be present in this class of devices.