We have identified spectral features in the late-time X-ray afterglow of the unusually long, slow-decaying GRB 130925A using NuSTAR, Swift/X-Ray Telescope, and Chandra. A spectral component in addition to an absorbed power law is required at >4σ significance, and its spectral shape varies between two observation epochs at 2 × 105 and 106 s after the burst. Several models can fit this additional component, each with very different physical implications. A broad, resolved Gaussian absorption feature of several keV width improves the fit, but it is poorly constrained in the second epoch. An additive blackbody or second power-law component provide better fits. Both are challenging to interpret: the blackbody radius is near the scale of a compact remnant (108 cm), while the second power-law component requires an unobserved high-energy cutoff in order to be consistent with the non-detection by Fermi/Large Area Telescope.