Misaligned Content when updating Design in InCopy

Does any one else ever have this issue? It does not happen to all pages, only a few every now and then.

After setting things up in Indesign and sending over to Incopy for Editors, sometimes content misaligns on a handful of pages. Not all of them, just a few sometimes. On some pages the guides become misaligned as well. The misalignment seems to be consistent with the amount of offset of the misalignment between the pages it happens on. Any idea where this could be coming from? No items are associated with any object styles so positioning rules are not a concern.