Magnetic doping is expected to open a band gap at the Dirac point of topological insulators by breaking time-reversal symmetry and to enable novel topological phases. Epitaxial (Bi(1-x)Mn(x))2Se3 is a prototypical magnetic topological insulator with a pronounced surface band gap of ∼100 meV. We show that this gap is neither due to ferromagnetic order in the bulk or at the surface nor to the local magnetic moment of the Mn, making the system unsuitable for realizing the novel phases. We further show that Mn doping does not affect the inverted bulk band gap and the system remains topologically nontrivial. We suggest that strong resonant scattering processes cause the gap at the Dirac point and support this by the observation of in-gap states using resonant photoemission. Our findings establish a mechanism for gap opening in topological surface states which challenges the currently known conditions for topological protection.