Large deletions and rearrangements of the plant’s genome, which can involve thousands of base units of DNA, have been observed following CRISPR gene editing.

Biswas S et al (2020). Investigation of CRISPR/Cas9-induced SD1 rice mutants highlights the importance of molecular characterization in plant molecular breeding. Journal of Genetics and Genomics. May 21. doi:10.1016/j.jgg.2020.04.004.
This study found that CRISPR gene editing in rice varieties caused a wide range of undesirable and unintended on-target and off-target mutations.

Höijer I et al (2021). CRISPR-Cas9 induces large structural variants at on-target and off-target sites in vivo that segregate across generations. bioRxiv. doi:
This study shows that CRISPR-Cas gene editing in zebrafish caused large structural changes at on-target and off-target sites (both at the intended edit site and elsewhere in the genome).

Kosicki M et al (2018). Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements. Nature Biotechnology 36:765–771.
This research shows that CRISPR/Cas9 gene editing can cause greater genetic damage than was previously thought. Many CRISPR-edited cells had large genetic rearrangements such as DNA deletions and insertions. Potential consequences in gene therapy include triggering cancer.

Mou H et al. (2017). CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion. Genome Biology 18:108. DOI: 10.1186/s13059-017-1237-8.
This study in human cells unexpectedly found large deletions resulting from single CRISPR-induced cuts, in some cases in excess of 500 base units of DNA. In some cases, subregions of genes (“exons”) that carry information for the protein(s) for which they encode were deleted. This resulted in the formation of novel gene structures encoding truncated forms of proteins. Truncated proteins in food can potentially be allergenic or toxic.

Shin HY et al. (2017). CRISPR/Cas9 targeting events cause complex deletions and insertions at 17 sites in the mouse genome. Nature Communications 8, Article number: 15464. doi:10.1038/ncomms15464.
The researchers found that CRISPR editing resulted in unexpected types of indels (insertion-deletion mutations) at all 17 sites in the mouse genome that were targeted. Depending on the site, the size of the deletion was unexpectedly large – up to 600 base units of DNA. Such large deletions from a single CRISPR cut had not been clearly defined in previous studies. The authors mention that this was because the technology that is generally used to determine the extent of the deletion (known as polymerase chain reaction or PCR) had not been appropriately applied; that is, the PCR analysis was used in such a way that it would only detect small indels.