The main problem is random mutation. As the copy number increases and the host cells are passaged, the more opportunities there are for new mutations to arise, especially without any selection on the GOI. The integrity of the cloned GOI is assured by quality control at each step using sequencing. The biggest risk is probably if the GOI ends up having a gain of function mutation that is deleterious in the target organism.

According to my knowledge, the most appropriate method to access the accuracy and reliability of gene cloning is DNA sequencing.

The risks associated with gene cloning include nucleotide deletion that can be deleterious for gene function and the substitution of a few nucleotides with others that depends on the fidelity of the DNA polymerase used for the amplification of a particular gene.