The photos probably don't show the problem very well... I presume it's the pink-ish colour you mean?
If it's actually that colour, could be a pH issue? (unlikely)
Also has the appearance that maybe if using a 4 jet wand the middle two are blocked. Check them!
Could be disintegrating underlay been sucked up, or even dust/crap from under the floorboards been sucked up. In either case the only real way to sort it would be to lift the carpet, put some polythene sheeting between carpet & underlay and re-clean.
Also has the appearance of UV damage from the photos but you normally wouldn't get it come up any worse from cleaning, it should have been like that already. The only possibility with that - and this has happened to me - is that there is more than one colour of fibre used in the yarn. UV can degrade the same fibre at different rates according to the dye used to colour it.
I've cleaned a carpet that was a mixture of red and blue - the red fibres literally were all breaking up and getting extracted whereas the blue stayed firm. This gave an overall impression when you stood back that the affected areas were much darker. Looked like they were still dirty but obviously that wasn't the case.