Hello Jj5685,
Was your leather dry when the spots appeared? In my experience I've only had mold spots (and what you describe does sound like mold) when the leather has still been wet. Once it's dried out again I haven't experienced mold showing up on it, but I live in a very dry climate. If you live in a humid climate maybe that could be a problem. I have had specs like that show up from a reation to steel that leather naturally has when it's wet, and lemon juice does make those disappear too. It could be possible your specs showed up because something got on the leather.
Lemon juice does a pretty good job taking off small specs of mold. I've had luck with denatured alcohol too, but I think my favorite for really cleaning is oxalic acid. You can probably find this under a brand name of 'bar keeper's friend' at your local hardware store. It is also called wood bleach. It's a strong cleaner and is traditionally used by leather workers, just remember that both oxalic acid and alcohol dry out the leather a lot and you will need to add conditioners (neatsfoot oil or whatever you normally use) afterward. I believe that once you clean a project with the oxalic acid, the mold won't come back, but that's just my opinion. I've only been doing this for a few years so I could be wrong.
Bob