A client asked us for 4 x A5 designs to be printed.
They supplied us with .ai files and linked .pdf 's.
When we printed these designs and box appeared, which was not visable on screen, it produced a darker shade of green in this area. 

To rectify this problem:

Changed the linked .pdf into photoshop file. 
Because I found out when certain photoshop files are exported into .pdf only certain versions (adobe pdf 1.4, 1.5 and 1.6) can be imported into illustrator.

Imported the new photoshop file into illustrator

Traced the image (using "Colour 16" settings and changed the number of colours up to 50)

Expanded the illustrator points and deleted surrounding white spaces

Saved it as a new .ai file ready for importing into InDesign to be lay-up for print