As far as the machine flexing, if that's the case, it's doing the exact same thing on every identical part. (I have 5 of the same parts all being cut out of 1 sheet of MDF. The "notch" is the same size on all of them, and right where it plunges, no matter the orientation of the part on the MDF (if that makes sense). Thanks for the replies so far!!
That would be expected. Machine flexing doesnt have to mean the actual frame or gantry of the machine it can be backlash, the spindle or its bearings. Plunge moves put the most stress on a cutter as it has a flat bottom and tries to wander. If you dont believe me it out by putting a cutter in a hand drill and try to drill a hole through some wood
Lead ins like Tweakie mentioned may help, doing a ramp into the material instead of a plunge likewise or if you have to plunge then do a finish pass.
Hood