Those lighter patches are evidence of the stain not being "taken up" in those particular spots. For some reason in those areas the stain did not penetrate. The most likely cause is residual glue in the wood fibre. You can open up those fibres gently using a brass toothbrush, and re-apply the colouring in those areas carefully to blend them out.

Id be tempted to attempt another application on the right hand side of the body as well, as that slab is considerably-lighter than the other.