I have created a model in ModelBuilder which does the following;
uses the feature classes iterator (the feature classes have varrying numbe of fields)
uses the make feature layer tool
uses select by location tool
feature class to feature class tool (this writes the selected feature classes into a feature dataset)
For reason I do not understand not all the fields of a feature class are created in the last step.
I have also attached the model as a graphic
From your image, it looks like Feature Class to Feature Class didn't run (no grey drop shadow under the tool).
I have often looked at the output of a previous run from a model I have created thinking this run gave the same results.
Do you have overwrite output set in your environment?
Are you running the model from ArcMap, and do you have fields hidden in your layer?