Flatt's score at the 2010/2011 GPF: 127.57
Flatt's score at Skate America, 2012: 136.09
It's more than one bad year, imo.
Host picks are selected first and there were no TBAs, so when Flatt was chosen, even Ashley didn't have two spots yet.
Rachael was still in the top 10 for season's best in the 2010-2011 season, thanks to her performances during the GP season.
2010 NHK 161.05
2010 Skate America 162.86
2010/2011 GPF: 127.57
2011 Worlds: 154.61
2011 Skate Canada 128.22
2011 Cup of Russia 147.63
2012 Skate America 136.09
So it's more like bad year-and-a-half.
And since host picks are chosen first, it's likely that Rachael was chosen because it was assumed that Mirai would get two on her own because of her being #11 on the SB list. Who knows maybe USFSA was just as surprised for all we know.