Usually, if you apply stain to the end grain of a board it will turn out to be much darker than the face of that same board. That's because the end grain quickly soaks up much more stain that the face in the way a dry sponge soaks up water. To get a closer color match between the face grain and end grain try paritally sealing the ends before applying the stain. You can use several different things to do this: white or yellow wood glue diluted with water and brushed on, shellac, or a commerical preparation like Minwax Pre-Stain Conditioner. If you can, do some testing on pieces of scrap wood to see what works best. Apply your choice of sealer, let it dry, then apply stain to both the face and end. If the end grain is too light, thin the sealer by adding water or the appropriate solvent. If the color is too dark, try applying a second coat of sealer.