What have I missed here?
To be so direct, but this is a typical "bad tutorial" case where people always use adjustment layers instead of applying effects directly to layers. Conversely, things like collapsed transformations and so on just like 3D itself inflence the render order, so instead of following rubbish YouTube tutorials or whatever you might want to go back to the source and read the help section on that stuff and how to structure your project so everything works as you may expect it, including additional levels of using pre-composing if need be.
it's hard to know exactly what are you dealing with without a clear screenshot of your composition and timeline but let me share this piece of knowledge: usually when you make adjustment layers, you want them to be 2D and not 3D, you generally don't want adjustment to float in 3D space. also you generally don't want adjustment layers between your 3D elements (whether they are 2D or 3D) because they break the 3D interaction.
See if this workflow advice solves your situation:
1. if you have color adjustments - make them on the layer itself and not with adjustment layers.
2. if you do want an adjustment layer to affect all the composite below it, make it 2D and above all your stack of layers in the timeline
if you want more specific assistance, please provide us some screenshots and try to visually describe your problem.
I've only used adjustment layers for the background.
All my other colour adjustments are placed directly on the pre comps. Do I have to go in and apply on each individual asset?
See my comment. Using collapsed transformations and the like will still change render order and neutralize specific effects. in any case, without seeing screenshots of your timeline and comp in order to understand what you are actualyl doing, nobody can tel lyou more than that and we're all just guessing around.