Here's the relevant paragraph from the article:
If Snowden’s sample is representative, the population under scrutiny in the PRISM and Upstream programs is far larger than the government has suggested. In a June 26 “transparency report,” the Office of the Director of National Intelligence disclosed that 89,138 people were targets of last year’s collection under FISA Section 702. At the 9-to-1 ratio of incidental collection in Snowden’s sample, the office’s figure would correspond to nearly 900,000 accounts, targeted or not, under surveillance.
They use this information from Snowden, the 160,000 intercepted messages, showing that nearly 10 people were targetted "incidentally" for every 1 legitimate target. With that 10 to 1 ratio, and a transparency report released in june showing that there were almost 90,000 legitimate targets, the math comes out to approximately 1 million Americans "incidentally" targetted.
Of course it's a crock to say these people's communications were spied upon "incidentally". They were explicitly targetted for incidental reasons such as being in the same IRC channel, using a foreign IP address, etc.
What I don't get, though, is that the list of "minimized" targets whose identities were scrubbed as being likely Americans includes "a sitting President". Does this mean they spied on President Obama's communications, and then scrubbed his identity from it? Were these legitimate targets sending threatening emails to thanksobama@whitehouse.gov or what? Did they scrub any reference to his name, even when it didn't involve communications originating from him?
How did he wind up as any of these "incidental" targets?