This is not really an ACF question, it is a question about creating archive pages by in WP.
When you load the URL for a CPT or a Term in a Taxonomy associated with that CPT WP has already done a query based on the CPT and the Term if applicable. Your query is overriding the query that WP already did.
I would suggest the you look at pre_get_posts for and the WP template hierarchy rather than creating custom queries.
