As I said why can you? it is inconsistent with the rules you are using.
To find E with a guassian surface, you are essentially integrating over the field E. This is the field that exists. The integrand is dot product of the field and area vector normal to the surface. So when you have determined the field using this method, you cannot add anything to it or double it after the fact. That is incosistent with your integrand assumption in the first place.
The only trick in all these problems is to use symmetry to simplify the integral.
To help your understanding try doing this, think of a single plate (infinite if need be) with surface charge sigma, take a gaussian surface around it. ie reactangular box with faces parallel to the plate and infintesimal thickness in the normal direction to the plate).
The symmetry here, is the same magnitude field will be out of the faces on both sides, normal to the face, if a face has area A, then
\int E_{1plate}.dA =2E_{1plate}.A = Q_{enc} = A.\sigma
Giving
E_{1 plate} = \frac{\sigma}{2}
When you add a 2nd plate with charge -sigma, the field outside is given by:
\int dA =2E_{2 plate outside}.A = Q_{enc} = 0
So
E_{2 plate outside} = 0
Now to calculate the field inside, go back to the previous guassian surface enlcosing one plate only:
\int E.dA =A.E_{2plate} + A.E_{2 plate outside} =E_{2plate}.A + 0 = Q_{enc} = \sigma.A
So the field is double that of a single plate inside & zero outside, if that is what is throwing you off, but still only sigma
E_{2 plate} = \sigma = 2.E_{1 plate}