Inline entity form only makes the connection to some structure and displays it, it doesn't change it. In your case the Inline entity form is showing the Create node form of a certain type (you haven't mentioned which type is in your case), but you can't change the structure through the Inline entity form.
If you want to add a User reference field to that node type you have to go through Structure > Content types > [Your type] > Manage fields.
There you can add a new field (or use an existing one if it makes sense to your structure) of the type Reference > User.
Once you add that field when you go to created nodes that reference that node type through the Inline entity form, you will see the User reference field among the fields after clicking on "Add new node".