Hi @Nimaxim : All of the things mentioned in the other posts are at play here. First I need some further clarity:

1. The inputs are the several X's (what you are calling "factor values")

2. The response Y comes from a NN model that is/was built based on those same several X's (as in 1 above)?

3. Then you are using a multiple regression/response surface to model Y (which is output from a NN model as in 2 above) as a function of the same X's (as in 1 above)? i.e., you are trying to predict the output from a NN model with a multiple regression/ Response Surface model (6 linear effects, 6 quadratic effects, and 15 interactions to make up the 27 model degrees of freedom)?

Do I have that correct?

If so, your results are not surprising. There is no pure error (i.e., replicates give identical results), so the only source of error is due to model misspecification (lack of fit). Before we get too far down this road...why are you doing this?