Hi Javier,
Yes your intution is correct. fitnet have some preprocessing and postprocessing involved. These processing functions are captured in the layer properties of the network.
For example, You can see the preprocessing of input by accessing Input layer, Giving a code snapshot for you to try.
% Process function
net.inputs{1}.processFcns
% Process function parameters.
net.inputs{1}.processParams{1}
and the same way you can access processing function for every layer(also output layer).
Try doing it, you will be able to get the correct answer.
Cheers.