Single-molecule junctions are found to show anomalous spikes in dI/dV spectra. The position in energy of the spikes are related to local vibration mode energies. A model of vibrationally induced two-level systems reproduces the data very well. This mechanism is expected to be quite general for single-molecule junctions. It acts as an intrinsic amplification mechanism for local vibration mode features and may be exploited as a new spectroscopic tool.