I work at a radiology facility. We have a machine that is a PET/CT scanner (a hybrid machine) which can perform both exams at the same time. However, some facilities perform the exams on separate machines.
These two tests provide slightly different information. The PET scanner usually identifies abnormal cell behavior (the injection helps highlight these areas). The CT scanner gives a more precise location of different masses, cancerous or otherwise.
Doing both the PET and CT scans give a better overall picture of what is going on. I would just call your oncologist (or whomever referred you for the scans) and discuss the results with him/her.