Statistically, it is extremely improbable that the morning-after pill (which is a very high dose of hormonal birth control) could be abortive. The chance is not zero, but it is possible that it could be taken in such a way that it fails at preventing ovulation (depending on where the woman is) or preventing fertilization (the other most common effect) but somehow works to prevent the fertilized egg from implanting. This is technically possible, though only if taken very late relative to sex (near or past the end of the 72-hour window).
The morning-after pill has NEVER been stated to act on an implanted embryo, which is what this story claims. If this is true, this would be a scandal of massive proportions. The way this story is written makes the events impossible by known science. It’s most likely misreported and the truth is probably the woman took not the morning-after pill but an actual abortifacient like RU-486.
The morning after pill makes the woman shed the lining in her uterus because of the massive dose of hormones. If there is an embryo that is beginng to attach it would cause it to be shed too.
No, what's going on here is that LifeSite is deliberately misusing terms in order to excite their largely ignorant readership, which will then provide LifeSite with more revenue. Read the article again. The claim is that the clinic "implanted" the embryos, and an hour later, told her the wrong embryos had been used and offered her the morning-after pill. No clinic has the capability to "implant" embryos, and no embryo has the capability to implant within an hour of being transferred (or of arriving naturally) into the uterus.
The woman had a loose embryo floating around in her uterus, and the morning-after pill ensured that it would never implant (though there was a much better than even chance that it wouldn't have implanted anyway).