Spot re-staining a shelf post poly?
Are you saying the stain area was damaged and then poly was applied over it?

If so, there are no options. (none that do not involve sanding).

Post photos to get more experienced opinions &amp; thoughts on this statement/answer: 

If the areas are noticeable but not to an obnoxious level (right where everyone will stare all of the time), you could spot treat the area by sanding with a small tool and then stain, clean, and re-poly.

BUT it will be noticeable, so would the poly repair so: You'd light sand the surface (the entire surface) and clean, then run a new poly coat. That will help the poly/surface blending. 

The stain repair WILL be noticeable (although you could possibly make it look like a natural defect in the wood). Take time when repairing to make sure the edges are treated such that you do not get a thicker border that looks like a coffee spill.

In general, you will have to decide if this is worth the time and fuss to do, or if a surface strip and re-apply is the right approach.

The advice for poly and stain and having clean surfaces includes inspection. This is something I'm sure you wish you had noticed before proceeding. Hopefully the idea above can help?