I haven't worked with label printing and I am sure there are several of us who are just like me. Can you explain what you have to manipulate in an Illustrator file to get it to print on a label (flexo press). Perhaps this will help the rest of us understand what is needing to be done to our files.
Sorry to interject, but answers to this question could possibly save gazillions of dollars and also put me out of work once and for all.
This question ought to have it’s own thread and I can’t even scratch the surface, but many things are often needed to be done to prepare supplied "print ready" files: from minor text editing (if required) and removal or remapping of colors, to adjusting percentages in gradient backgrounds, manipulating or resizing graphics and placed images and their windows for template accuracy (as John W. just mentioned); and not to mention, adding or adjusting holding lines, ko’s and built-in traps for these images.
Fortunately, I have a “make it nice” button on my keyboard that automates most of these and other processes.
And NOT to say that Indesign can’t do all that’s needed, but I too am more familiar and prefer Illustrator for labels, packaging, and many page layout jobs as well.