You should be able to sand it out unless it is part of the natural wood. Then, re-stain it. If it has already been sealed, this will be difficult to blend.

It is a pinewood using mahogany MinWaxx stain- our painter said it is from the wood itself. It has not been seal or Poly- do you think it is a worth to try to re sand and stain or just completely paint it?

If it's part of the wood, then it cannot be fixed because it's likely all the way through the wood. It looks like a stain to me though, which means someone splashed something on the raw wood. We see this all the time really...even delivering raw wood in the rain can cause this. It sands out pretty easily usually and then you can touch it up with the stain. It's worth a shot. If you are unhappy with the repair then you can always paint it.