If parts are cut to the exact size on the CNC, then they will likely not fit. If a mortise is 18 mm wide and you try to put a 18 mm thick tenon to make a joint, then the wood will likely splinter or you will not be able to fit the parts together at all.
It is important to allow for some clearance in between the pieces. Generally it is easier to add clearance in pocket cuts since the nominal thickness of the plywood is static and stays the same.
Adding Clearance in Fusion 360
Clearance is added after the model is complete. In Fusion 360 there are two ways to add clearance for pieces to fit together. The model can be modified so one part is physically smaller than its “nominal” dimensions. This can be useful for fabrication methods such as 3D printing. The second method is to remove a bit more material when cutting the parts out. In the pocket cuts, for example, entering a - negative stock to leave number will cut away more material and create a gap.
Before deciding on how large of a gap to create for part clearance, it is helpful to run a test cut with a particular machine and material. Create a series of pocket holes of the same size for a part to fit into. Then increase the amount of extra stock removed in each pocket hole. After cutting, test which clearance amount gave the best fit with space for glue and use that for the complete model.