Sorry to say, it has happened to my Palermo PM - both on the short handle side facing the jeans and the piping at the bottom corner. I was able to reduce the marks on the piping using a white eraser. The handles - I just let them, since they will darken eventually in time. I've had mine for over a year but don't use it that often.
It may depend on your jeans, if you notice - some brands include a tag with a warning on dye transfer. It can happen on any model where the vachetta rubs against clothing.
I love my palermo and like using it best hand-held. But when I need my hands free, I use the neverfull, which you may want to consider since it is vachetta free for most part or consider a bag in damier ebene.