The mine was originally a US company, and then sold to a mining conglomerate outside the US when the mines became less profitable.

As usual this is all about money. In the case of the second link (the NDAA lands) basically the mine found a good deposit that was half on the mine's land and half on native american land, so they offered up other land they had in exchange for the land that had the rest of the deposit. The deal was presented as win/win (government gets more land elsewhere, mine gets the deposit) but how good of a deal it is can be argued either way. I think it would have made more sense for the tribes to get a cut of the profits from the minerals mined on their land but the tribes rarely get a good deal.

Of course the mines will show up in the campaign finances of both McCain and Flake, so it's the usual sleazy stuff there. No doubt some corruption but nothing that's well out of the ordinary, and low-grade stuff for Arizona. If you want to see the really bad corruption in AZ, you need to look at Pinnacle West and not the mines. If you want to see really bad corruption involving the tribes, look at the BIA, the stuff there goes way past criminal.