In this paper, a practical approach to the trajectory design for asteroid exploration missions with CubeSats is presented. When applied trajectories are sought, operative concerns and uncertainties affecting the spacecraft dynamics must be considered during the design process. Otherwise, trajectories that are possible on paper might become unfeasible when real-world constraints are considered. The risk of such eventualities leads to the urge of extending the trajectory design focus on the uncertainties affecting the dynamics and on the operative constraints derived by ground operations. This is especially true when targeting highly perturbed environments such as small bodies with low-cost solutions as CubeSats, whose capabilities in deep-space are still unknown. The case study presented is the Milani CubeSat which will be launched in 2024 with Hera in the frame of the AIDA mission.