The question I have is, what version of WP to you start on when you started making updates? Was it 4.3 or lower?
This reminds me of a split terms issue. In WP4.0 and earlier a term ID could be shared across taxonomies, so if there was a “Business Category” and a “Post Category” that shared the same name they would actually have the same ID. This was changed over several version until at WP4.4 terms were completely split during the WP update.
On top of this term meta was also added during this change. Before this ACF stored values for terms in the options table and ACF was updated to save values to the term meta table.
So, if you updated from WP4.3 or earlier then you are probably suffering from one or both of these issues.
