Just throwing this out there to see if anyone with the same problem can offer some advice.. Happens with all dyed and unwashed denim, but hasn't really been addressed here.
Some of the indigo dye on my N&Fs rubs off onto the shoe tongue. Not a problem on darker shoes, but on the white tongue it can be sort of a hassle. Warm water and soap has been my go-to, and prevents the problem depending on what surface your stain is on.
Edit: After searching around a bit more it seems that this problem is basically unavoidable. Gonna go with the "tape your cuffs" trick and see how that works.
You could always try a soak and get ride of some of that excess indigo. Also, what kind of shoes are we talking? I've had a lot of luck cleaning my white canvas Purcells and Vans by doing an overnight OxyClean soak.