I've tried to run games (in a couple systems) that had complex NPC factions to engage with, and a lot of players just... don't. I think sometimes they just don't realize it's an option.
My last game was kind of picking up speed, where there was a bad megacorp (within it two main factions) and a fractured array of resistance groups. I was hoping the players would do some alliance building. It was kind of working, but then real life sort of scuttled the game.
The other problem that happens to me a lot is I think about the game between sessions, and the players don't. They don't remember much detail. So I'll be like, "And you discover he's been working with the Seers the whole time!" And they'll be like "the who? Is that bad?". It's hard to get factional stuff going if the players can't keep straight who's who.