If this is a new machine have you calibrated your machine. Even if you machine were out of calibration it would be consistently out of calibration for all parts but that could lead to your pieces not fitting together perfectly. Also remember wood is an imperfect medium. Generally plywood is stable but wood does move and is susceptible to moisture. Take a look around on cutrocket.com and on this forum for projects and see how they cut their tolerances.
Also, John Clark has a YouTube channel with videos showing how to built various boxes, and the principles of interference fit of the lid and base of a box is demonstrated well (I think) in this video for a heart-shaped box.
I’ve used this video to design and make my own very simple boxes (including a heart-shaped one).