Ulhumbrus: The pair of moves 15..Nxd4?! and 16...Qxd4? constitute a very serious positional mistake, a mistake which turns an advantage for Black into a possibly winning positional advantage for Kramnik.
The lesser reason for this is that the first move of the pair, the move 15...Nxd4?! opens the c file. The greater reason is that the second move of the pair, the move 16...Qxd4, exchanges the Queens and so removes them from the board.
The first result of the removal of the queens is that White is rid of his most serious liability, an uncastled King which is exposed to attack.
The second result is that after the exchange of Queens, the evaluations of the position become all reversed, as if by magic.
All of White's liabilities become transformed into assets, and all of Black's assets become transformed into liabilities. Targets for Black targets become transformed into weapons in the hands of White.
The c file, instead of exposing White's King to attack with queens on the board, becomes after the exchange of queens, a weapon in White's hands. White's advanced King side pawns become transformed, after the exchange of queens, from targets into a weapon. White's King becomes transformed, after the exchange of queens, from a target into a weapon.
With the c3 pawn transferred to d4 and the White King safe, Black, instead of having prospects for a Queen side attack or for a King side attack, has passed the initiative on both wings to White, who threatens now to use both the c file and a King side pawn advance to attack Black.
Instead of 15...Nxd4, The right move is 15..0-0-0 with ...f6 to follow after which Black seems to gain the advantage. White seems unable to maintain even equality against Black's potential threats of ...f6 starting an attack along the f file and an attack upon the d4 pawn by the manoeuvre ...Ng6-e7-c6.
Possibly one way of putting this is to say that the effect of the pair of moves 15...Nxd4?! and more so that of 16...Qxd2+? is to remove White's most serious liability, an unsafe King. The removal of this liability makes the difference between Black having the advantage and White having a possibly winning positional advantage.
Leko probably did not realise in time the full consequences of exchanging the Queens upon the evaluation of the position. Perhaps he was concentrating on other aspects of the position at the time.