ACF updates both fields, the problem is that if there is a duplicated field on the page that the second field will overwrite the first value. This is not something to do with ACF, this has to do with the way WP stores values in the database.
I don’t think it’s really possible for ACF to keep track of all fields and let you know when there is a duplicate.
There are also times when you want duplicates, or at least there is for me. I use the same field name for the same type of field used for the same purpose in different field groups associated with different post types so that I can right code once that will work for the field on all post types and in all templates where I need to use it.
It’s basically up to us to make sure we don’t use duplicate field names for any field on the same WP object.
