Chuck has it right! Spots that vary from light blue gray all the way to black are a result of a reaction between the tannins in the leather and iron contamination. It could have happened anywhere after tanning until it arrived on your bench.
A year or so ago, I had a nice piece of leather that was going to be part of clutch purse with horses figure carved on both sides of the purse. I cased and transferred my pattern onto the leather bagged it over night. In the morning, I came back to it and there was this blue spot outside of what would be the carved area, so couldn't be hidden with tooling or dye. There was a tiny piece of metal embedded in the leather just below the surface. So it had got there during the tanning or finishing process.
Like Chuck says, keep all iron filings and fleeings (fine particles of metal dust in the atmosphere) away from your leather and off your bench. Even turning on a fan could be enough to blow iron dust laying on any surfaces around your work space.
As a matter of interest, you can look up vinegaroon, used to 'dye' leather blue/black. It's really not dye, but a chemical reaction.