Live from a GP Milan Trial:

Neo has a Kiora with a dice on it, showing 1. Anderson attacks it with a 2/1.

At the damage step, it appears that Neo's Kiora should have 3 counters, as he played it on the last round and used the +1 ability. He says that the dice represent the extra counter (in addition to the two base loyalty shown on the bottom right), and that he put it when he played her ability.

Anderson agrees with the sequence of events, saying that he did not remember which ability was the +1 and which one was the -1 and that he assumed that Neo put directly the resulting loyalty, as players are wont to do.

What would you rule?

There is a specific exception in the IPG for representing game state in a seemingly unclear way so long as it is clear to both players. In this case, it was obviously not clear to both players, so this is an actual Game Play Error.

GRV + FtMGS, either rewind it or let the game stand.

A very similar call occurred during GP Phoenix; there was a bit more time elapsed, but it became clear to me (after talking to both players) that the attacking player made decisions based on the “1” loyalty on his opponent's planeswalker. When the opponent confirmed that it was just a momentary lapse of reason, putting a “1” to +1 it, instead of the resulting loyalty, I ruled that loyalty would be treated as 1 and the game would continue as is.

d:^D

Scott, is the ruling that the player paid the wrong cost or just that the player placed the incorrect number of counters? Not that it changes the situation, but I'm curious

Incorrectly represented derived info - i.e., the wrong number of Loyalty counters were shown, and allowed to persist long enough to influence decisions.