The action of the gene editing tools is not the only cause of genome disruption. The gene editing process, taken as a whole (including plant tissue culture and GM transformation procedure), induces hundreds of unintended mutations throughout the genome of the plant. This can affect multiple gene functions with unknown consequences to protein biochemistry and metabolic activity.
Tang X Tang X et al (2018). A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice. Genome Biology 19:84. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1458-5 While this study found that the CRISPR tools in themselves did not introduce many off-target mutations in the rice plants, large numbers of off-target mutations resulted from other aspects of the CRISPR genetic manipulation process – namely tissue culture and Agrobacterium infection. (When making CRISPR’d plants, tissue culture is always used and Agrobacterium infection is commonly used to deliver the editing tool.)