GC/MS analysis is only as good as the machine used, and the analyst who interprets the results. Some chemicals are present in an Essential Oil or a Fragrance at such low levels that the detector used in the analysis cannot "see"it. There a very strong smelling chemicals which are present at very low levels that are important for the overall smell, but cannot be detected unless specifically looked for. The GC traces of Bergamot and Petitgrain are fairly similar; indeed adding 10.0% Petitgrain to Bergamot will not alter the GC trace significantly. However, the odour of Petitgrain and Bergamot are vastly different; mainly due to the presence of Pyrazines in the Petitgrain. Very strong smelling, present at very low levels. There is a technique ( called Smelling GC) where one can smell each chemical as it is separated by GC. Our noses are not very good at measuring how much is there, but they are very good at detecting what is there.
If your two analyses of the same sample show such different results I would question the machine or the analyst. You are sure that exactly the same sample gave two such different results?