Cunha was back in the starting XI for the match at the Gtech Community Stadium, where the Reds fell two down in the opening 20 minutes, following a brace by compatriot Igor Thiago.
Benjamin Sesko halved the deficit and Bruno Fernandes missed the opportunity to equalise from the spot, before Mathias Jensen sealed the win for the Bees in stoppage time.
There were calls in some quarters for Brentford captain Nathan Collins to be sent off, after he pulled back Bryan Mbeumo for the penalty, but Cunha felt that the Reds did not do enough over the course of the 90 minutes.