There's nothing wrong. Whatever particle system you used is an effect that only does its magic inside the layer, not the comp. Imagine it like a window into a 3D world, but not an actual 3D world. If you want to retain the 3D-ishness, you will have to use such stuff in the main comp directly. An alternate way is to link stuff across comps with expressions to sync cameras and motions and use the nested layers as 2D layers. Of course they won't interact with the main comp correctly, too....
Been scratching my head on that for days as I'm used to Maya modelling and need to think more in a semi 3D perspective for AE.
But that means if I have multiple stuffs going with a main composition, the project gets very messy to manage, isnt it? Is there a way to then group them under one? But I guess the best way is replicate the original content in the composition, edit it and pre-comp it into a new comp within new project is the easiest way to manage project file in AE?
I was thinking of creating a generic composition that I can migrate to use repeatedky elsewhere really.....
"Messy" is a very relative term as is "Main Composition". I never found this to be any issue and I'm happily pre-comping Particular and other stuff all the time. There is no magic recipe and I find that a lot of this simply depends on your experience level vs. the specific requirements of a project. The real trick is to simply keep things separate to a point and in fact not trying to do everything in one bold stroke. Many people are simply getting too wired up over that 3D stuff too early in the process and then get themselves in all sorts of pinches because despite some Particular fairy dust the rest of their project is 2D stuff, if you get my meaning. Or in other words: It's all about structuring your work suitably. If you can provide more specific info on the project. I'm sure there's some pointers we can offer...