It sounds like the area wasn't properly sanded - perhaps not fine enough in this area, so the stain didn't absorb the same as the rest of the area.
If that's the case, you'll probably need to refinish the whole area - at least the whole room (assuming there is a saddle or clean breaking point at the end of the room (or else you could add one). You can't just resand a section and you can't just apply more color to a section, esp once the poly has been put on top.
Debbie Gartner aka The Flooring Girl
http://TheFlooringGirl.comWestchester County, NY