I did use a sanding block on the sides.
looks like they are HIGH spots,,,, ( I ) would just stain them over again,,,and call it done
Lighting and angle makes a difference in how obvious these splotches are. From some angles they all but disappear and from others they are obvious.
I had a few spots like that when working on my 38-8 cabinet. I sanded lightly with 800 grit sandpaper to ensure it was smooth, and just hoped toner would cover it. It did, looks fine now- you can't even tell.