Throughout Crimson Peak Thomas was helping or working with some people on a machine which digs red stuff out. What was that red stuff and what's the significance of it to the film?
What was that red stuff..
Edith and Sir Thomas eventually marry and return to England. They arrive at Allerdale Hall, the Sharpes' dilapidated mansion, which sits atop a red clay mine.
The wiki page on Red clay (disambiguation) suggests it may have been useful for pottery.
what's the significance of it to the film?
Not sure, but note that crimson is a "strong, red color, inclining to purple". And that it has connotations of anger or embarrassment when applied to people. E.G. "He turned crimson when his tryst with the student was revealed to the rest of the faculty".