The master tools seem to simply indicate that tehy are very limited but are more likely to get you a lot of extra mats out of nodes. There is no indication that there are resources that they will not farm properly, however they do not harvest a number of higher tier mats.
I have seen sickles fail on raspbetrries and many things above, and know that the pickaxe will not farm Orichalcum. This is a very frustrating issue as the nodes are rare and the item doesn’t say it will not work with them, so there is a heavy incentive to save your master harvesting gear for these very lucrative nodes.