illustrator transparency

If your RIP supports transparency you can use the PDF/X-4a export setting from InDesign and you won’t get those lines.

As John said above, what you are seeing is Transparency Flattening, which is a result of Illustrator trying it's best to display and output foreign Transparency. You're best off opening the PDF in Acrobat and outputting the file from there.

As a side note, you will also see these "cut lines" when InDesign Exports a PDF to a version earlier than Acrobat 5, because transparency was not supported before that version.

You'll have to provide more detail as to exactly what you're attempting to do with this.

If it was created InDesign, and you exported a PDF which you subsequently opened in Illustrator, that is not an intended workflow, and the tiled-and-stitched result you're getting would be no surprise. That's not "Illustrator Transparency," it's the mess of clipping masks you get when you open an alien PDF in Illustrator. The only PDF's Illustrator can parse predictably are those it created.