You have not provided any info about your comp, your settings, what version of AE, screenshots and so on, so pardon me, this is pointless. Chances are you use Collapse Transformations and make a mess or you have not been working in the active camera view or something liek that, but we really can't know...
If you have the Composition Panel set to anything other than Active camera we need to know more. If you are looking at the Active camera here's my first guess. You used Camera Tracking and did not set origin so when you added the camera and another layer the camera was pointing way off in space somewhere. When you turn your Pre-comp 3D it is at the comp center and 0 Z. Your camera is pointing somewhere else.
The fix if you have a 2 node camera is to open up the camera properties and find the point of interest. Copy those values and paste them to the position of your pre-comp.
The other option, depending on how far along you are with your comp, is to set an origin in Camera Tracker to get the camera pointed at the right space then add your camera.
My second guess is that you did not use Camera Tracking but have pointed your camera off in another direction so it is no longer pointing at the comp center. The comp center is the center of AE's world and that's where every layer ends up when you turn it 3D.
There is one other option, you have 3D layers inside your pre-comp and you have turned on Collapse transformations. That combination puts the 3D layers out of the camera view.
If you had provided a screenshot with all properties of all problem layers revealed by pressing the U key and a thorough explanation of your work flow to the point where you and the problem we could probably tell you exactly where you went wrong.