We study unconventional superconductivity in exfoliated single crystals of a promising three-dimensional (3D) topological superconductor candidate, Nb-doped Bi2Se3 through differential conductance spectroscopy and magneto-transport. The strong anisotropy of the critical field along the out-of-plane direction suggests that the thin exfoliated flakes are in the quasi-2D limit. Normal metal-superconductor (NS) contacts with either high or low transparencies made by depositing gold leads onto Nb-doped Bi2Se3 flakes both show significant enhancement in zero bias conductance and coherence dips at the superconducting energy gap. Such behavior is inconsistent with conventional Blonder-Tinkham-Klapwijk theory. Instead, we discuss how our results are consistent with p-wave pairing symmetry, supporting the possibility of topological superconductivity in Nb-doped Bi2Se3. Finally, we observe signatures of multiple superconducting energy gaps, which could originate from multiple Fermi surfaces reported earlier in bulk crystals.