The first thing that springs to mind is Abrash (sp?) This is where the wool is from 2 different batches, but dyed with the same dye. When new, the rug looks fine. As it ages, soils and fades, the different wool batches react differently. Hence the different shades. Sometimes it can even be in stripes.
The surprising thing is that, if this happens on a fitted carpet, it's regarded as a fault. On a rug it's all part of the character
Of course, without further information or an inspection, this is only an educated guess.
Safe and happy cleaning
Ken