You’re not going to be able to have both using a taxonomy field. The main reason for this is that you’re using a repeater so if you save and load the values each row in the sub field loads the terms and or save them, each changing the terms associated with the post.
To do what you want you’d be better off having another custom post type for ingredients and then using a relationship type field instead of the taxonomy field. Overall it will be a bit more complicated. Then users can pick an ingredient and see recipes associated with the ingredient.
If you want to do this you should look at http://www.advancedcustomfields.com/resources/querying-relationship-fields/
