Different sources of uncertainty in CFD simulations are illustrated by a detailed study of 2-D, turbulent, transonic flow in a converging-diverging channel. Runs were performed with the commercial CFD code GASP using different turbulence models, grid levels, and flux-limiters to see the effect of each on the CFD simulation uncertainties. Two flow conditions were studied by changing the exit pressure ratio: the first is a complex case with a strong shock and a separated flow region, the second is the weak shock case with no separation. The uncertainty in CFD simulations has been studied in terms of five contributions: (1) iterative convergence error, (2) discretization error,(3) error in geometry representation, (4) turbulence model, and (5) the downstream boundary condition. In this paper we show that for a weak shock case without separation, informed CFD users can obtain reasonably accurate results, whereas they are more likely to get large errors for the strong shock case with substantial flow separation. We demonstrate the difficulty in separating the discretization errors from physical modeling uncertainties originating from the use of different turbulence models in CFD problems that have strong shocks and shock-induced separation. For such problems, the interaction between different sources of uncertainty is strong, and highly refined grids, which would not be used in general applications are required for spatial convergence. This study provides observations on CFD simulation uncertainties that may help the development of sophisticated methods required for the characterization and the quantification of uncertainties associated with the numerical simulation of complex turbulent separated flows.