Guided-mode resonance (GMR) bandpass filters have many important applications. The tolerance of fabrication errors that easily cause the transmission wavelength to shift has been well studied for one-dimensional (1D) anisotropic GMR gratings. However, the tolerance of two-dimensional (2D) GMR gratings, especially for different design architectures, has rarely been explored, which prevents the achievement of a high-tolerance unpolarized design. Here, GMR filters with common 2D zero-contrast gratings (ZCGs) were first investigated to reveal their differences from 1D gratings in fabrication tolerance. We demonstrated that 2D ZCGs are highly sensitive to errors in the grating linewidth against the case of 1D gratings, and the linewidth orthogonal to a certain polarization direction has much more influence than that parallel to the polarization. By analyzing the electromagnetic fields, we found that there was an obvious field enhancement inside the gratings, which could have a strong effect on the modes in the waveguide layer through the field overlap. Therefore, we proposed the introduction of an etch-stop (ES) layer between the gratings and the waveguide-layer, which can effectively suppress the interaction between the gratings and modal evanescent fields, resulting in 4-fold increased tolerance to the errors in the grating linewidth. Finally, the proposed etch-stop ZCGs (ES-ZCGs) GMR filters were experimentally fabricated to verify the error robustness.