Chests with NBT data, or other machine / items that contains item data can bypass replicator blacklist.

I don't really see what can be done in that case tbh, but it is semi-intended that the replicator can most likely duplicate items contained by other items.

Pack creators can add whichever item tags they want to the replicator blacklist using KubeJS.

Going to close this as "works as intended" :P