This is definitely off topic for this site. Nevertheless, as others have said, it’s at least partly because your PCB is not as flat as you likely think. Lots of solutions - suggest you look elsewhere for details - particularly how to best secure your board on the mill. You can also probe the board area using the milling bit and run an autoleveling routine to adjust your Gcode. Have a look here for some useful tips autoleveller.
TBH, I’ve largely abandoned milling pcbs - it’s ok for non critical THT stuff - like making speaker crossovers, adapter boards etc. For SMD work with finer traces, it’s not worth the effort. Sure, it can be done but you have to have a very well controlled process. Boards are trickier to solder with no solder mask and prone to random shorts from whiskers of copper. Milling PCBs was one of the reasons I bought a small CNC machine a few years ago but nowadays I hardly use it for this any more.