My (admittedly poor) recollection of the scene is this:
- The camera is doing a visual close-up of the soil. I forget if this was the part showing small, flowing rivulets of black goo.
- The soil is visually barren (except for the goo if that is indeed this part).
- One of the human characters walks across the soil.
- As they lift their boot, a worm appears. I remember it as a centipede rather than a worm, but that's not too important.
So, was the worm in the soil and was exposed by the person walking over it? If so, why hadn't it become mutated at some point in the past? Or was it transferred from the person's boot, perhaps picked up from outside and stuck in the groves?