5 gallon extract kits are designed to brew a 5 gallon batch, but of that 5 gallons there is always a percentage of loss to trub from the primary (yeast and hop debris). Are you using a secondary? If so, there is potential for additional loss in the racking process as well as additional loss to absorption from dry hopping.
If you add additional water to your batch without adjusting the fermentables you will wind up with a lower gravity than intended while making up for the losses. The best thing to do is look at your racking process to be sure you are getting every bit of beer you can and be sure you are topping off to the proper level of 5 gallons. Also, when filling the bottles be sure you are consistently filling to the correct level and not over filling them.
IMO, it is better to get the beer you want than a few extra bottles of beer