Active flow control has been a growing research area for the last decades, since this approach demonstrated its ability to improve aerodynamic performance, for a large range of applications. It is especially appealing in case of separated flows, for which natural instability phenomena can be efficiently exploited to manipulate flow characteristics using periodic flow excitation. In this context, a major difficulty is related to the choice of actuation parameters, such as excitation frequency, amplitude, location, to obtain the expected flow response. In cases implying a single isolated actuator, it is quite easy to carry out an experimental or numerical study to determine efficient control parameters. However, in the perspective of industrial applications based on hundreds of actuators, this task is far from being straightforward and the use of an automated optimization strategy is thus proposed, in the spirit of previous works. While optimization algorithms are now commonly employed in aerodynamics for shape optimization purpose, their use in the context of control devices yields new issues, which are detailed in the present study. In particular, we aim at quantifying the impact of the numerical errors (discretization, convergence) and modeling uncertainties (turbulence closure) on the optimization procedure. The choice of the optimization parameters is also explored. Different test-cases and flow solvers are considered in this study, e.g. NACA airfoil, backward facing step, 25 degrees ramp.