I have a Doc Library using a custom content type with about 15 managed metadata fields in it.
For some reason filtering on one particular column whether it be MM Navigation, MM Key Filters, or just a basic column filter returns 0 results even though there is data that should match. Though fields added long before this one in particular still work.
Removing and remaking the field does not correct the issue. Even further, adding other MM fields to the content type makes them also return 0 results when filtering.
Lastly, I've tried making a new doc library and testing. No MM fields will work there.
I am able to produce this behavior across 3 different farms using the backup of this site collection.