Those are glue spots. Ideally, before staining, it's a good idea to wipe the bodies down with a damp cloth and look for any spots like these. Then you need to use something like a toothbrush and acetone to scrub it off. It's quite a common issue unfortunately. I have seen people do a pretty good job of disguising it with a marker. If it were me I'd sand back and start again, making sure to do a pass over the problem with some acetone.