The Si3N4 layers in a 3D NAND flash patterned wafer are generally removed by hot phosphoric acid. However, the abnormal deposition of silicate which is the by-product from Si3N4 etching onto the neighboring SiO2 layers will cause a serious problem in the subsequent process. In this work, the abnormal deposition phenomenon was investigated by a simple system containing a narrow gap (~ 80 μm) between two blanket wafers. To understand the mechanism, the influences of various factors on the chemical etching dynamics were examined, including the water content and the extent of mechanical agitation. It is found that the growth rate of SiO2 decreases as the water content or the extent of agitation is increased. Our experimental results reveal that the abnormal growth on SiO2 layers is a consequence of the competition between chemical deposition and mass transfer in a confined space (reaction–diffusion system).