Okay, I just ran that print - a bit smaller to fit on the chip - no changes to it except for changing the cut order on the circles to make them cut first, and I used my standard settings for that chip of 380/58.
All the circles cut out fine. What might have happened is - if you let the outsides of the squares cut first, the pieces might have shifted, and that might have caused some of the circles to not cut all the way through. You want to anchor it down as flat as possible for the little circles.
So you might want to try moving those to the top if you haven’t already done it.
Having said that - running that file caused one of the most frightening displays of travel speed on the part of the head movement that I’ve seen. It was shaking the table from the vibrations it caused. There is something wonky with the file - maybe because of the various conversions it went through, or maybe something in how it was created, I don’t know. If I could interpret the code for it I’d look for some kind of acceleration code in there…but not my bailiwick. Never seen it before. But that wasn’t normal movement.
I’d re-create the file from scratch rather than let that continue. But if you want to use that one, moving the holes to the top of the thumbnail column will let it cut through.