Those are going to show no matter what you do. If you bought a "kit" of bed wood, return those for a replacement, the quality of those boards is not acceptable.
If you prefer, you can fill the low spots but they will never disappear. My suggestion for the least noticeable filler is sawdust from the same wood mixed with wood glue. You can harvest sawdust from scraps if you have any or by sanding the bottoms of the planks with a hand held belt sander that has a dust collection bag. Or you can do it by hand, but the best way is with a saw because sanding will leave grit from the sandpaper in the dust. Since most belt sanders have black grit you'll wind up with tiny black specs in the dust.
Mix the dust with
ELMERS CARPENTER GLUE to a toothpaste consistency and use that to fill the holes. When dry it can be sanded smooth and stained or painted. It will show when stained but it will be the closest match you'll get.
But your best solution is to return the boards for replacements. Any carpenter would immediately reject those boards when buying lumber for a finished project.
