Are you working with conditions to show / hide fields, which have already an initial value?
If yes, the problem is, that the hidden fields are only disabled in the user interface, but for the report the hidden fields are still activated and have the value for it. We would recommend to re-build the necessary forms of your Workflow process and use the Dictionary integration. In the Process Manager you can create a new dictionary category with custom attributes. Afterwards, you can use this category in your form to get the necessary initial values in depending of the choosen attribute.