Plasmids are circular double-stranded DNA discovered in bacteria and modified into vectors for gene delivery that became an essential molecular foundation for Genetics, therapeutic compounds production, gene therapy, etc. Like restriction enzymes, DNA polymerases, and antibodies, vectors are among the most widely adopted tools in molecular biology research. Most of the tools have been standardized and commercialized for decades, yet vectors often need to be customized and constructed for a specific experiment. Although double-stranded circular DNA is biochemically stable, naturally occurring mutations accumulated in vector cloning and propagation are frequently overlooked. After analyzing about a thousand vectors from worldwide academia or industrial researchers, we identified that about 24-35% vectors contained point mutations in some key elements, such as open reading frames. About 15% of the vectors had significant structural rearrangement or mutations in cloning sites. Adeno-associated virus (AAV) is one of the most promising gene delivery tools, however the only cis viral element, Inverted Terminal Repeats (ITR), has high GC content and secondary structure making the element rather unstable. We identified that only 61% of AAV transfer vectors still maintain ITRs consistent with the original sequences. Through the comparison of the mutated and stable AAV vectors, we found how GC content on vectors could dramatically decrease the ITR mutation frequency from ~59% to about zero. Our findings ring an alarm that the issue of vector accuracy resembles the issue of mycoplasma contaminated or misidentified mammalian cell lines that have been reported recently. Unidentified mutation could substantially jeopardize the function of the vector and experimental results. To help improve vector accuracy, we describe a Good Vector Practices (GVP) system which we have implemented for years while generating over half a million vectors used for virus packaging, gene editing, mRNA, or recombinant protein expression.