Why do dark spots randomly appear on my Elisha?

I have no probs with my elisha (last years model), but my new bow wallet keeps showing spots/stains and I can't for the life of me figure out what in my bag is causing them!!
 
hmm did you guys all spray protect them before use with two coats? I'm guessing the elisha is probably just really delicate. I haven't used my red elisha enough to notice but I did protect her.
 
I have a Brown Isabella that have random dark spots appear since I got it. Not from handling or wear, they just show up. Luckily in this case it makes the bag look more Vintage and rustic so that's cool. I would not be happy if it happened with my Elisha.
Kooba keeps spreading the joy with their ever changing leather this season.
 
It's a new blue one. I've actually returned 3 of them to Neiman Marcus because of various problems... the one with the spots also had excessive dried glue around the seams. Not a huge deal, but for $500+, no thanks...
 
My red one had a spot appear AFTER I had protected it (twice) and conditioned it, etc. It was all dry and happy, and then like a day later "BOOM" - there it was. I hadn't even taken her out, she was in her sleeper bag.

It's not too bad, but WTH? Why would a leather do that?