Hi there. Yes, if I ever wipe a damp cloth on oak I get the same thing.
I agree with some of the posters here already: it's the tannins in the oak reacting with ferrous metallic particles. The reaction is brought about by the presence of water. It's the same process that causes oak to go dark (and almost black over the centuries), and the same one that causes a black circle if you leave a metallic (ferrous) pan on a wet oak surface.
I've wondered a few times about where the metal comes from for these black dots though. My guess is that it's either particles present in the water itself or it's particles in the workshop. That second one seems the most likely to me. Do you ever use steel wool? That stuff breaks into tiny, tiny pieces that will probably float about somewhere in the shop for ever more. I've moved over to using those plastic abrasive pads to try to minimise the amount of steel wool I use. Perhaps the same problem could come from microscopic steel flakes created during sharpening.
As for how to deal with it during glue-ups, you just can't use the wet cloth method to remove glue. Bummer, I know. Try some other measures, e.g:
- masking off the joints so that squeeze out goes on to the tape rather than the wood.
- wax the surfaces you want to protect before glue up. The glue won't stick to the wax. Here's how... Put the joint together dry, clamp it, rub finish wax all around the joint, take it apart and glue up, then when the glue dries the squeeze out will just flake off the waxed surfaces. You can remove the wax if required using white spirit before moving on to whatever finish you choose (just check for compatibility beforehand).
- use less glue so the squeeze out is less of a problem (or no problem at all). I struggle with this one

- or wait till the squeeze out is nearly dry and use a combination of card scrapers, chisels, etc. to remove it. It's a bit fiddly but sometimes it's required, as we no doubt all know
I'm sure there are other solutions though. I'd love to hear them too.
Cheers,
Ali.