Interactive PDFs are saved as RGB (for screen preview, naturally), and don't need to flatten transparency.
This article explains why you may see "ghost lines" onscreen but they won't print out:
but print PDFs have ghost lines?
For print use PDF/X-4, or if you have to flatten (PDF/X-1a) make sure your Transparacy Flattener preset used in the Export>Advanced tab has high enough resolution. Sometimes you have to change the raster vector balance to all rasters to get rid of "stitching"
So the default High Resolution might stitch:
While this 0 Vectors won't even though its res is lower