We have identified spectral features in the late-time X-ray afterglow of the unusually long, slow-decaying GRB 130925A using NuSTAR, Swift-XRT, and Chandra. A spectral component in addition to an absorbed power-law is required at $>4\sigma$ significance, and its spectral shape varies between two observation epochs at $2\times10^5$ and $10^6$ seconds 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 black body or second power-law component provide better fits. Both are challenging to interpret: the blackbody radius is near the scale of a compact remnant ($10^8$ cm), while the second powerlaw component requires an unobserved high-energy cutoff in order to be consistent with the non-detection by Fermi-LAT.