You might post a close up of the area with the group of spots. My first impression is that stray bits of glue got on the surface. Was it peel & stick and/or heat activated or did you use liquid glue?

Most likely some type of residue was left behind. You could try sanding them out carefully without sanding too deep. Or you could buy a stain pen and color in the spots then apply another coat. They seem small enough where it wouldnt be that noticeable.

Thanks for the replies. I have to agree the spots were very likely results of glue. I have tried scraping off the surface before restaining the spots but that didn't do any good. I suppose the glue bled from under the veneer so no matter how much I scraped, stain would not be absorbed. I did use a furniture marker to darken the spots but they are still pretty obviously. I have the same problem with a second panel even I did test for glue spots with lacquer thinner and scrap before the first coat of stain. The panels are top covers of an old sewing machine cabinet so the imperfections are probably perfect - to match the rest of the cabinet. :-)

these?

Here is a link that might be useful: brush tip markers

Yes. I have three of them in different brown shades. Even after scrapping the glue spots it would take only a tint. I believe the glue bled from the underside of the veneer so it wouldn't absorb any more color. It's not a big deal because the rest of the cabinet looks pretty worn too so they kind of match.