All four custom taxonomies have quite a few posts and pages under them, and they’re all published and set to index.
I’ve already taken care of what you suggested with those reference links. They’re excluded from the cache plugin now, and I’ve updated the permalinks.
Just to give you a heads-up, the custom taxonomy was created using the Advanced Custom Fields plugin, and the same term is being used for both posts and pages.
Do you think there might be any other reasons for this?