The last time i knew of this story was as an audiobook anthology. i listened to it about three or four years ago, but unfortunately this doesn't mean the story isn't much much older than this.
In this short story, a tunnel is being dug, and a fossil hunter is asked to look inside, where he finds small worm like thing.
The man is sitting on a pile of slag looking for fossils, and the workers digging a tunnel ask him to come look at something for them. There's a breach in the tunnel wall, it smells, it's dark, and there are worm-like things in there. The worm-like animals are 'a type never seen before' and the fossil hunter thinks they have evolved isolated from the rest of the world in the huge cavern they find through the breach in the tunnel wall.
Plot order as i can remember it: Starts with a man (A professor? Englishman, an older gentleman), sitting on a spool heap, searching through the rocks, looking for fossils. He then starts to eat his packed lunch while sitting looking at the tunnel workings. The tunnel is (I think) a new train tunnel being dug. A foreman then calls him over and asks his advice as a 'man of science' the foreman then shows his a sealed glass jar with a strange worm/insect inside. He asks if the professor knows what it is. He says it was found in the tunnel in a place where a blast opened up a whole in the tunnel wall. The professor and foreman then walk into the tunnel towards the breech. There's a bad smell. through the breech he sees a mass of writhing worms, or worm like creatures. My memory lets me down from here.
Its setting is Victorian i think, in England or maybe Wales.
I read this in an anthology, it was most like a 'best of the year' type anthology, either horror or sci-fi.