What CAM software are you using?
Likewise CAD?
I use Turbocad and Sheetcam on our plasma. When you have fully nested parts with multiple operations, it pays to check over everything twice. For each step. It's critical that the drawing be flawless coming out of CAD and has each process under a different layer name for us. Holes, scribe lines, profiles etc. Goof that up and it will not cut like you want it to.
Same thing in CAM.
Also not all of our parts have holes in them. We group a few that do have holes in them and then immediately following the holes for that group, it cuts out those profiles. That way there is very little machine travel doing those parts and the holes are more accurately placed.
If you let the CAM do it alone, then it will kind of jump all over in order to help eliminate any sheet warpage. That can induce small errors in positioning if the table isn't perfectly accurate. Ours is pretty good, but not perfect. Rack and pinion.