If by "they" you mean Tarkovsky, sure; Stalker doesn't have much to do with the book, and hardly any plot elements survive. However, there is an explanation for it.
Tarkovsky originally shot the film based on a screenplay by the Strugatsky, an adaptation which was, I believe, quite faithful to the novel (this is not inconceivable, considering that Solaris was fairly faithful to Lem's story). But during post-production, the negatives were handled by an inexperienced lab worker who managed to damage the negatives beyond repair.
Tarkovsky fought to find funding to re-shoot the whole film, but at this point he was bored with the material, and essentially improvised the whole shoot based on his own ideas. The Strugatskys were not happy with the final film.
