Hello,
As it's said on the documentation
That option enables you to change the options of the filters according to the previously selected filters. For example, if all your products are computers with 4Go Ram and 250Go hard disks, if you select 4Go in the first filter, the second will show only the 250Go option and not the other values.
The problem is probably coming from the combination of value selected through your filter custom field and also from the fact that some combination aren't available so some value aren't displayed.