Honestly, it just seems like the enemies the PCs faced just weren't properly designed to be a significant obstacle.
Consider that at Rank 4, the PCs' foes should generally be whole armies and/or Greater Daemons.
A small group of essentially normal humans, therefore, won't be much of a challenge for Rank 3 PCs, without some significant modification to them.
Generally, at rank 3, the PCs would be delving into the dark depths of the Empire, rooting out and facing significant threats like Vampires, Lesser Daemons, groups of Trolls, Giants, etc.
If you want humans to be a challenge, you need way more, or you need to tweak the humans. Make sure to give NPC humans (especially bosses) their own Action cards, ones ranked up properly. They should have extra Training dice. IF need be, actually make the NPCs using the rules for PCs. 4 rank 3 PCs vs 2 rank 3 NPCs and some extra minions, should be a decent battle.