An initial metabolic reconstruction of a genome is typically far from perfect due to the high variability and diversity of microorganisms.  Often, metabolic pathway databases such as KEGG and MetaCyc will have "holes", meaning that there is a conversion from a substrate to a product (i.e., an enzymatic activity) for which there is no known protein in the genome that encodes the enzyme that facilitates the catalysis.  What can also happen in semi-automatically drafted reconstructions is that some pathways are falsely predicted and don't actually occur in the predicted manner.  Because of this, a systematic verification is made in order to make sure no inconsistencies are present and that all the entries listed are correct and accurate.  Furthermore, previous literature can be researched in order to support any information obtained from one of the many metabolic reaction and genome databases. This provides an added level of assurance for the reconstruction that the enzyme and the reaction it catalyzes do actually occur in the organism.
Enzyme promiscuity and spontaneous chemical reactions can damage metabolites. This metabolite damage, and its repair or pre-emption, create energy costs that need to be incorporated into models. It is likely that many genes of unknown function encode proteins that repair or pre-empt metabolite damage, but most genome-scale metabolic reconstructions only include a fraction of all genes.
Any new reaction not present in the databases needs to be added to the reconstruction. This is an iterative process that cycles between the experimental phase and the coding phase. As new information is found about the target organism, the model will be adjusted to predict the metabolic and phenotypical output of the cell. The presence or absence of certain reactions of the metabolism will affect the amount of reactants/products that are present for other reactions within the particular pathway. This is because products in one reaction go on to become the reactants for another reaction, i.e. products of one reaction can combine with other proteins or compounds to form new proteins/compounds in the presence of different enzymes or catalysts.
Francke et al.  provide an excellent example as to why the verification step of the project needs to be performed in significant detail. During a metabolic network reconstruction of Lactobacillus plantarum, the model showed that succinyl-CoA was one of the reactants for a reaction that was a part of the biosynthesis of methionine. However, an understanding of the physiology of the organism would have revealed that due to an incomplete tricarboxylic acid pathway, Lactobacillus plantarum does not actually produce succinyl-CoA, and the correct reactant for that part of the reaction was acetyl-CoA.
Therefore, systematic verification of the initial reconstruction will bring to light several inconsistencies that can adversely affect the final interpretation of the reconstruction, which is to accurately comprehend the molecular mechanisms of the organism. Furthermore, the simulation step also ensures that all the reactions present in the reconstruction are properly balanced. To sum up, a reconstruction that is fully accurate can lead to greater insight about understanding the functioning of the organism of interest.