This sounds more like an issue with the software used to perform the cut.
As Illustrator was initially created for the print industry, you can utilize the same workflows, by either separating cutting steps by layers in Illustrator, or using spot colors to define each printing plate (or step in your cutting tasks).
Depending on the version of Illustrator, there may be scripts to export each layer as a file (if not, do so manually). From that, you may be able to load each exported file to your cutting software.
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