The reason for this, is because in reality when performing chemical reactions, the moles or the molecules of the reactants actually do not react completely based on stoichiometric amount or mole to mole, this can be because, there is much solvent present, or the molecules do not possess enough kinetic energy to collide and form new bonds.
Not enough heat was used for instance if it were to be an endothermic reaction.
Also there may still be impurities in the reaction vessel, especially with the reactants that have been prepared and now are performing the reaction with.