Alteration of the genetic code of the targeted gene can produce mutant forms of the protein it encodes for, new RNA, and new protein products. These outcomes can lead to changes in the plant’s biochemistry and the possible production of novel allergens and toxins.

Mou H CRISPR gene editing for gene therapy applications can cause massive damage to chromosomes. The phenomenon is known as chromothripsis. The fact that the damage occurs “on-target” – at the intended edit site – means that any attempts to target the CRISPR gene editing more precisely will not solve this problem.
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1237-8

Tuladhar R et al (2019). CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation. Nature Communications vol 10, Article number: 4056, 6 Sept https://www.nature.com/articles/s41467-019-12028-5
This research investigated outcomes in human cells when CRISPR was used to knock-out a gene function by disrupting its normal base unit sequence. The study found that instead of the intended outcome of destroying the function of a CRISPR-targeted gene, in 50% of cell lines investigated, the indels (insertion-deletion mutations) resulted in an alteration of the gene’s DNA base unit sequence, so that it now produced new types of mRNAs (messenger RNA molecules) or proteins.

Smits AH et al (2019). Biological plasticity rescues target activity in CRISPR knock outs. Nat Methods 16, 1087–1093. https://www.nature.com/articles/s41592-019-0614-5
This study in human cells revealed a major unintended effect from the CRISPR-Cas9 gene-editing tool. CRISPR edits intended to knock out the function of a gene failed to do so. Instead, proteins were still produced from the damaged genes. Many of those proteins were still functional, but they were also mutant, which means they could gain a novel function, with unknown consequences.