Collection of gas over water
You are right! There is an approximation here in only considering the vapor pressure of the gas. But let's consider the value of vapor pressure of water at $298\ce{K}$:  it's  $13.85\,\ce{mm Hg}$. So, if you neglect the vapor pressure of water, the relative uncertainty is  $$\frac{13.85}{760}\times100=1.83\%$$
As you can see, it's negligible.

P.S. To calculate the vapor pressure of water, I used the first equation in http://en.wikipedia.org/wiki/Vapour_pressure_of_water