This is a little pet-peeve of mine: Never does Seacrest say that the two left standing on the stage on elimination night are the lowest two vote-getters. With all due respect to the hard work the writer of that article has done, he or she is incorrect in that assumption. The line to the first of the three to sit down is, "...you are safe," not, "...you have the third lowest votes." The producers decide which two of the three contestants left have the biggest drama associated with their fate and leave those two on the stage (to take us into the break!).
The only time we know which contestant is in the bottom two is by the time AI leaves only two on the stage, instead of three.
I think what the author is saying is that Fantasia was in the bottom 3 TWICE, weeks 6 and 9. That author left out commas and such, so I took it as hurried writing. just a guess