Okay so before I went to bed last night I had a look at my shoes. They were stuffed with newspapers but they made them lose their shape. So I replaced them with shoetrees, put them on their sides on a bookshelf and then I went to bed. Woke up around one hour ago and this is how the most saturated shoe looked like
Does this look good?
They look better than I thought, but pictures lie.
I'd give them another 24 hours. Put a *tiny* bit of reno on the area where you had dark spots and see if the leather darkens. If so, you have the same issue I did with the shoes in the link above: they looked OK when dry, but any moisture at all brought out the darkened spots.
Others here might tell you how you can fix or minimize it. I just went in the direction of darker polish and waterproofing for the future.
As a side note, if the newspaper was making the shoes lose their shape, you were using too much. The point is to put enough in there for absorption and a bit of structure and leave them on their side for a while. I'd probably take the trees back out, put some newspaper in and lay them on their side again for a few hours just to see how dry they are inside.
Net: you want to make sure they're entirely, 100% dry before doing anything else.