Where are the spots coming from? This is one of the first questions many new woodworkers ask. After having just completed building their first masterpiece they're shocked when they apply stain and light colored blotches appear out of nowhere. This is often caused by small amounts of glue that get left on the surface and prevent stain and finish from penetrating the surface.
“Squeeze outs”, glue finger prints, and drips are often the culprits. Every woodworker runs into this problem at some time and many professional woodworkers are paranoid about searching for glue spots before finishing.
One good way to locate them is to wipe down the surface with denatured alcohol. The alcohol evaporates quickly and the temporarily “wet” wood will be darker except where the glue remains. A cabinet scraper (click here for more information on cabinet scrapers) or a little sanding will often take care of the problem.