In one scene, Ron Perlman's character is eaten by a giant monster. This isn't the first time this has happened to him in a del Toro movie, it also somewhat happened in Hellboy. Was this scene supposed to be an homage to Hellboy, or am I reading too much into it?
During the scene after the end credits, we see Perlman cut his way out of the Kaiju and then exclaim "Where's my Damn Shoe!?"
That whole bit where he gets swallowed (by a premature Birthed Kaiju with no teeth) was simple comedy relief scene to show that the character portrayed didn't know everything, but maintains posturing as though he does.
I doubt this was a nod or anything like that to Hellboy.
From the Wikipedia page of the movie:
Del Toro wanted to "honor" the kaiju and mecha genres while creating an original stand-alone film, something "conscious of the heritage, but not a pastiche or an homage or a greatest hits of everything". The director made a point of starting from scratch, without emulating or referencing any previous examples of those genres.
It doesn't refer Hellboy but it explicitly says that Del Toro doesn't want to pay homage to any film. Rather than popular culture, he drew inspiration from works of art such as Francisco Goya's The Colossus and George Bellows's boxing paintings.