Possible answer something called wicking
what happens is the stain is caused by a large spill, you clean and the mark goes away, but as there is still some of the spill in the backing as the carpet dries it wicks back up and becomes visible again.
Remedy = go back and clean again give extra attention using handtool rather than wand and give a good flushing thru, as this problem usually occurs whilst drying it would also help to force dry using turbo dryer if possible, that way you know once you leave the mark is gone for good.