I mean yeah, why wouldn't someone calling someone else an NPC use popular-thing™ as their basis for an insult?

Although it is also a common thing to have more characters in a game than can be properly fleshed-out, and AI is commonly shoddy (or just limited by the technology/scope) too. And a shortcut or joke that was funny at first wears out the 100th time.

Tie this in with said characters often having generic names/tasks and I'd guess that people probably aren't thinking about/referring-to well-written characters (particularly with dialogue/cutscenes etc) as NPCs.