When you first load an archive with a taxonomy filter, any terms that are not assigned to posts will be omitted from terms offered by the filter (because they cannot produce results), if the setting “Show only filter options that would produce results” is applied.
This fails if the taxonomy is also used on other post types, and a post of some other type has the term assigned. Then the term will be erroneously included in the filter.
We recently did some work to optimise these queries (which can be expensive on larger sites), but that has introduced this problem. The developers are aware of the issue and will review.