Saving a particular field of a related entities with Entity Reference
I think the content is saved correctly but displayed wrong. Try to change your View which displays the results (the table). On the field for the entity reference, you should have an option to change the Formatter of the displayed entity. I think you have currently "Rendered entity" selected. Try to change to Label to only show the title of the referenced entity. 



You could also display a different View mode for the rendered entity to show more/different fields. Check the Display Suite Module for this.