To upgrade weapon mutator you will need corrupted lumenite crystals and scrap.
Corrupted lumenite crystals can be found after beating Aberrations.
Aberrations are a more powerful versions of enemies and can be found in all worlds. You recognize them by having an health bar at the top of the screen and one or several modifiers (drain, regenerator, hearty...).
Here the list of Bosses belonging to Aberrations :
Losomn
Grime Crawler (Butcher's Quarter/Cotton's Kiln)
The Executioner (Council Chamber/The Great Hall)
Ripsaw (Morrow Parrish)
Firth: The Oathkeeper (Malefic Palace)
Barghest the Vile (Harvester's Reach)
N'erud
Abomination
Fetid Corpse (Void Vessel Facility)
Restless Spirit (Terminus Station/Tower of the Unseen)
W.D. 109 (Void Vessel Facility/The Putrid Domain/Vault of the Formless/The Hatchery)
The Progeny (The Hatchery/The Dark Conduit)
E.D. Alpha (Tower of the Unseen)
Yaesha
Defiler (Forgotten Field)
Rot (The Chimney/The Twisted Chantry)
Wither (The Lament)
Mantagora (Imperial Gardens)
The Weald Stalker and The Gnarled Archer (Forgotten Field/The Expanding Glade/Imperial Gardens/The Nameless Nest)
This guide has been made with the help of the Remnant 2 Wiki.