The noise analysis in spectre (and indeed other simulators) compute primarily the noise at the output of the circuit, from all noise sources in the circuit. The only reason for noise not being included is if the noise on that component has been specifically disabled (for example, the instance parameter isnoisy=no has been set). The way it works is to compute the magnitude of the noise at the noise source (i.e. at the device) based on the bias point (if that matters - for example, for shot noise), and also compute the transfer function from the noise source (i.e. at the device) to the output. The noise powers at the output are then summed, and the total output noise computed.
The input referred noise (which is a secondary output) is computed by taking the total output noise, and dividing it by the gain from the output back to the input that you specified on the noise analysis.
If your circuit has attenuation, then the input referred noise at the input will be larger than at the output.
You can use the noise contribution table (Results->Print->Noise Contributions) or the results browser to look at the noise contributions (at the output of the circuit) from each noise source in the circuit. This is a useful debugging tool to find out where the noise is coming from (or not!).
You could also compare the gain with (say) an xf analysis to see what the gain is in the circuit, so you can see if it is attenuating. If it's not meant to attenuate, maybe you specified the wrong nodes, or maybe the circuit is not biased properly (so check the operating point; it's amazing how often people don't check that, and commonly do things like forget to connect the supplies up. We've all done it!)