Dark Stain on Grenson boots: what is this?

[tauben]

I just cleaned my shoes this morning: I used a conditioner, tan polish and leather fat for the finish, all just in small amounts. In terms of what I used I did nothing wrong I think, but after I was finished there was a slight discoloration on one shoe. I hope the picture shows this. Is there a way to remove the discoloration? Or will it fade away naturally over time?