Definitely mold. Which is gross, and a pain to clean up, but there are some things you can do. It was always there, so don't worry that you made it worse, the mold would have surfaced eventually, bath or no bath. Since you say that it had small spots pre wash, the mold was already existent.
I have dealt with mold on a
coach bag or two. First, do not condition it until you kill the mold spores otherwise it will just come back. Start with a clean(bathed) bag, treat, then condition. Vinegar straight will kill most mold. Get some cotton pads and regular white vinegar and soak the spots suede side with vinegar. Make sure you really soak it so that it can penetrate and kill the whole spore. Wipe the smooth side of the leather with vinegar but do not soak as much. There is also a product that is non toxic that kills and treats mold (keeps it away) called concrobium mold control (spray) that you can get at home depot. I used it as a final treatment on a particularly musty moldy bag and it has kept it from any further damage/growth.
Treat with vinegar and let dry completely - sun is also very good for killing mold. You can't just rely on sun though - you do need the vinegar. After you have treated all of the bag and it's dry, then you can condition. As a final step I used the concrobium spray dabbed on the suede side. The dark spots may have permanently stained the leather, but a conditioner that darkens leather may help it blend in. A good one is leather therapy (
amazon), which also has anti mold agents in it. Mold is no fun, but there are fixes. The bag may look great when you are done with it!
Oh - forgot - when re-bathing I rinse the bag with some vinegar in the rinse water. It doesn't hurt the leather at all.