Trapped-ion crystals are a leading platform for quantum information science, but achieving the high-fidelity entangling gates required for fault-tolerant quantum computing becomes harder as system size increases. As trapped-ion processors scale and adopt new geometries, spectral crowding makes low-order nonlinear resonances between collective motional modes more common and can limit gate performance, especially in monolithic and global-mode architectures. We develop a general model to identify and simulate nonlinear motional-mode coupling (NoMoCo) arising from third-order anharmonic terms, primarily from the Coulomb interaction, and quantify its impact on the M{}lmer–S{}rensen gate across linear chains and two-dimensional crystals in rf and Penning traps. We identify regimes where NoMoCo can produce significant gate errors and provide design rules: detune operating points from low-order resonances, tune trap anisotropy to reshape spectra, cool spectator modes, and shape gate waveforms to reduce bus-mode excursions.