Quantum transport in magnetic topological insulators reveals the strong interplay between the magnetism and topology of electronic band structures. A recent experiment on magnetically doped topological insulator Bi2Se3 thin films showed the anomalous temperature dependence of the magnetoconductivity while their field dependence presents a clear signature of weak anti-localization [Tkac et al., Phys. Rev. Lett. 123, 036406(2019)]. Here we demonstrate that the tiny mass of the surface electrons induced by the bulk magnetization leads to a temperature-dependent correction to the pi Berry phase, and generates a decoherence mechanism to the phase coherence length of the surface electrons. As a consequence, the quantum correction to the conductivity can exhibit non-monotonic behavior by decreasing the temperature. This effect is attributed to the close relation of the Berry phase and quantum interference of the topological surface electrons in quantum topological materials.