I'm not sure on the filly, but I have a solid palomino which has started to show some odd darker patches on him too... I don't think I have photos though, I should try to get some. I actually thought it was some form of countershading, or bend-or spots. D
He has some interesting white hairs coming through in patches too (originally I thought scars since he's forever getting nicks... But some are in places he was never injured, even minorly). I am not sure if he is a sabino, or something else (he does have a faint star and a couple socks paired with a couple partial coronets), but it is interesting.
Not a palomino, but we have a light bay with a dark bay spot too... We have had it suggested that it is a birthmark. We couldn't see it in his foal pictures and it wasn't part of his registration ID until we had it updated, but we assume it was there. He was a very odd looking bay foal (light bay along his topline but an odd mousy silver along his barrel) Has your filly had these marks her whole life or are they new? Maybe they are a birthmark of some sort?