I had a chest of drawers made of pine that had crayon marks on it. I sanded it down really well and applied a coat of golden oak stain after puttying the holes. Now there are light and dark spots showing through the stain. What did I do wrong?
Pine is notorious for needing to be sealed before staining. The wood soaks up stain too much. Hence, any impurities (e.g. old glue from incautious gluing), or areas of high sap concentration will vary how much the stain gets soaked in.
At this point, you need to sand the whole thing down to wood, apply a wood conditioner (probably on the shelf right next to the stain), and re-stain. If the wood is really sappy, you may actually need to varnish it instead as Rain said, as you can't just sand through that. Be especially conscious around knots as the stain take-up will be very different there.