No one is happier than I am to see the New York Times do an extensive piece debunking the myth that emergency contraception works, either primarily or secondarily, by killing fertilized eggs. The actual scientific evidence plus pre-existing knowledge of how hormones affect the body has long pointed to ovulation suppression as the only possible way that emergency contraception could work. Despite this, anti-choice activists and politicians have gone out of their way to confuse people about the difference between emergency contraception and abortion. Their excuse for why they "get" to lie to the public about this has been the packaging that states that hormonal contraception might also work by preventing the implantation of a fertilized egg. Even though that's not abortion—abortion terminates pregnancy, which begins at implantation—for the anti-choice crew, that was good enough to justify the lie.
That language on packaging for emergency contraception reflects a period before the research confirmed what scientists already suspected, which is that ovulation suppression was the only likely function of these pills. It reflects a tendency in science not to rule out any possibilities until you have to, and was never meant to be used as a political weapon by people who don't believe a woman has a right to reject the almighty seed after a man has deigned to place it in her body. Unfortunately, the constant conflation of contraception and abortion has gone mainstream, creating widespread confusion over exactly what a woman is doing when she swallows Plan B.
Unfortunately, despite the Times best efforts, I expect that the confusion will continue. Part of the problem is just scientific ignorance. The popular understanding of how pregnancy works in our society is a male-oriented one, where people assume the magic moment happens pretty much when a man ejaculates. Getting people to understand that it's more like three to five days after you have sex is hard to do, since it counters their "common sense", i.e. male-centric view of reproduction.
But the other part of the problem is that the anti-choice movement deliberately sows confusion on this, and just because their lies have been debunked in the paper of record is hardly reason to think they'll grow more shy with the lying. After all, the claim that abortion causes breast cancer is still flung around shamelessly, no matter how many times a year scientists disprove it. There's no reason to think they'll suddenly grow respectful of actual science now that it has shown that emergency contraception has no effect on egg cells who've had their good Christian souls injected into them by those emissaries of the Lord known as sperm. As the past two years have demonstrated, flinging the word abortion around in order to attack contraception access is a remarkably effective anti-choice tool. They're not going to let a little science get in the way of a deal like that.