OK, so someone decides to duplicate himself 100 times.
In Canon it has occurred twice once to Kirk and dogalien, once to Riker. The Kirk one was a personality disorder. So if Mr. Clever pulls it off you then advise him is 100 copies are defective. One does nothing but scream, another cry, another scratch another roll on floor and on and on and on.
GM's job is to police things and keep Jackwagons from ruining things. You don't always have to say no, you can just monkey wrench them too depending on the 'violation' they commit. Godlike is hardly Trek except from the shows NPC's, Metrons, Trelane/Q, Thasians, Organians all put a stop to things they didn't like or humiliated the crews to keep their ego's in check.
Replicators can't synthesize certain elements, so if someone wants X, it replicates faulty if at all.
In a decent Trek game Phasers work both ways, PC's can be vaped as easy as a mook. Tracy killed thousands but eventually his phasers drained.
Keep in mind even reboot-Trek can out clever itself.
https://www.youtube.com/watch?v=4N15J4ibej8