When you define cut paths in Adobe Illustrator with both Stroke and Fill these paths can end up as two identical paths in the exported PDF. When there are duplicates in the preview, you might see a missing path or the inverted cut job, e.g.:
Expected preview:
But the preview shows duplicates circles / missing holes:
Or, the outline is duplicated. The preview shows only the holes and a bit of the outline:
When you observe this in the 3D preview, it's usually an indication that there are duplicated paths in the input PDF, and thus with duplicated cut paths in ProCut.
When you define cut paths in Adobe Illustrator with neither Stroke nor Fill these paths will not be in the exported PDF. Thus, it is not possible to see cut paths in the cutting preview.
When you use spot colours to define cut paths in a multi-page PDF, all paths from all pages that are coloured with those spot colours are used as cut paths for the application. This can give unexpected results, e.g. if you have the same shape on two different pages. In that case you will have duplicated paths, both in the cut job and in the 3D preview. If possible, select a layer in the PDF that only contains the cut paths.