Exactly so. Chan had unwittingly performed a 4th combination, making the entire jumping pass invalid. Instead of coming closer to a silver medal, he barely eeked out his bronze.
This post is not an attempt to consider the fairness of the placements at this year's GPF, however, but more about the implications of penalizing invalid elements. I think there are two questions that should be answered: first, should skaters be punished for a mistake generally made in the heat of the moment? And, assuming one believes they should, is the current method of handling such jumping passes fair?
Invalid elements, known informally as Zayak rule violations (so named for 3T queen Elaine Zayak), have cost many a skater placements. Evgeni Plushenko famously suffered one of his two losses in the four seasons leading up to the 2006 Olympics when he did a third combination at the 2003-4 GPF; at the time, two was the maximum allowed. Daisuke Takahashi lost what would have been his second Worlds medal after attempting too many combinations in the LP at 2008 Worlds. Kiira Korpi had a jump invalidated at the 2012 Europeans, though in her case it was due to having too many repeated triples rather than an extra jump combination. Chan's only loss in the 2010-11 season came at the Rostelecom Cup, when multiple falls and an invalid combination dropped him to second, behind Tomas Verner. Most famous for his propensity for excessive combinations is Nobunari Oda; in fact, Chan even quipped that he had "pulled a Nobunari" at the GPF.
That's one combo/sequence too many, Mr. Oda. Again.
Skaters should be expected to know the rules, and indeed most of them manage to survive seasons and careers without any Zayak violations. That said, I feel that invalidating entire combinations when the violation is actually on one jump is excessive. Such errors are often due to a fall or a major mistake on what should have been a combination, leaving skaters scrambling to make up for their error. And just as skaters might forget to add a rotation to a spin, resulting in a dropped level; or to hold a position for the correct period of time in a lift, leading to either a lower level or an extended lift deduction, the error is not meant to break the rules, but a mistake made by skaters who are perhaps distracted for a moment.
So my suggestion is quite simple: if skaters still get partial credit when doing too much or too little on other types of elements, give them partial credit for the extra combination/sequence; namely, give them the points for the part of the combination that is not invalid. Give Chan his 2A and take away the 2T, give Takahashi his 3Lz and take away his 2T, and so on. Reward them for the jump that was not against the rules, and penalize only the part that truly did violate them. I'm even willing to accept something similar to sequence scoring for the valid part. Another possibility would be to give skaters who perform an invalid element a fixed deduction, as ice dancers get for extended lifts.
This should maintain some balance between ensuring that skaters follow the rules while also having the punishment fit the crime, so to speak, when they don't. And maybe we can finally leave the matter of Nobunari Oda's arithmetic skills behind us.