When you create a PDF through an Automate workflow and open it up in i-cut Preflight, the paths, layers, etc all appear correct. However, when you open the same PDF in Adobe® Illustrator®, elements are missing and there are additional paths where the "hole cut" layer is as well as another path where the cut path is.
Some elements are missing. Extra paths show up.
You would need the PDF Import for Adobe® Illustrator® to open a Normalized PDF in Adobe® Illustrator® and have the file look correctly.
If you do not have this plugin, and a Export to PDF at the end of your workflow, then open that file in Adobe® Illustrator®. It should look better. However, there are still some PDF objects missing from the file as Adobe® Illustrator® cannot import this correctly. One of the examples is that you won't have any Layers in Adobe® Illustrator® after importing a native PDF. So, this should only be seen as a workaround. Right way is to import a normalized PDF via the PDF Import for Adobe® Illustrator® plugin.