We present the results of inelastic x-ray scattering for magnetite and analyze the energies and widths of the phonon modes with different symmetries in a broad range of temperature 125 < T < 293 K. The phonon modes with X(4) and Δ(5) symmetries broaden in a nonlinear way with decreasing T when the Verwey transition is approached. It is found that the maxima of phonon widths occur away from high-symmetry points, which suggests the incommensurate character of critical fluctuations. Strong phonon anharmonicity induced by electron-phonon coupling is discovered by a combination of these experimental results with ab initio calculations which take into account local Coulomb interactions at Fe ions. It (i) explains observed anomalous phonon broadening and (ii) demonstrates that the Verwey transition is a cooperative phenomenon which involves a wide spectrum of phonons coupled to the electron charge fluctuations condensing in the low-symmetry phase.