The affected terms exist in more than one category.
My guess is that this has something to do with term splitting. This started in 4.2 and was forced in 4.3. What this means is that WP looks for terms that are in multiple taxonomies. If it finds any it splits them creating two terms with the same name but they now have different term_id values.
If you edit a term or category you will see the term ID in the URL, for example
All of the data is in there but it’s now associated with the wrong term ID, so ACF can’t find it.
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