This behavior is correct. It may be hard to understand why at first, so it helps to know about the rendering order used in After Effects and what Collapse Transformations really does.
First, remember that for AE, 3D space all takes place on 2D planes. The popular term is “postcards in space”. When you pre-comp 3D layers, that comp becomes a flat postcard inside the 3D space of the master comp. If you now rotate or move the pre-comped layer in 3D, the 3D perspective of the layers inside the pre-comp will be lost.
What happens with pre-comps is that AE renders everything inside a pre-comp before it renders the pre-comp with the rest of the master comp.
That is, of course, unless you have the Collapse Transformations (aka Continuously Rasterize) switch turned on. The CT pulls the layers in the pre-comp out and renders them with the rest of the layers in the master comp. This means, among other things, that 3D layers in the pre-comp can interact in 3D space in the master comp.
In your particular case, Yussef, it’s hard to say what the solution is without looking at your comps and the order you’re using. But if you have vector art that you want to continuously rasterize but also need to pre-comp in 3D space, you should just need to turn on the CT switch for the layers in the pre-comp, and then the CT switch for the pre-comp itself in the master comp.
Also, keep in mind that when you pre-comp, choosing the “move attributes” or “leave attributes” options are going to have a big effect on how the layers behave.