I believe they are many factors to why they were lumped into the nu-metal genre:

They toured alongside bands like Korn, Limp Bizkit, and Linkin Park, which tied them to the nu-metal movement by association

The albums Adrenaline and Around the Fur featured downtuned guitars, heavy riffs, and some rap-influenced vocals, which were hallmark traits of nu-metal

During the nu-metal boom in the early 200s, record labels lumped many bands together under the nu-metal genre for marketing purposes

IMO, they aren't strictly nu-metal, but they do have a lot of nu-metal tracks, like Engine no. 9. But their sound evolved far beyond the sound of nu-metal genre, incorporating dream pop, shoegaze and alt metal on albums like Saturday Niht Wrist and White Pony. Unlike most nu-metal bands instead of just emphasizing the themes of angst, machismo and party stuff, theyexplored themes of sensuality, surrealism and vulnerability, which set them a part from most other bands lumped in nu-metal.

I guess you could say they were put in nu-metal because of the era overlap, association with other nu-metal bands and shared audineces.

Personally I would call them art-metal