That data is only people who have signed up for plans, not those who are actually covered. From the glossary at the bottom:
The cumulative metric represents the total number of people who have submitted an application and selected a plan, net of any cancellations from a consumer or cancellations from an insurer that have occurred to date. The biweekly metric represents the net change in the number of non-cancelled plan sections over the two-week period covered by the report.
To have their coverage effectuated, consumers generally need to pay their first month’s health plan premium. This release does not report the number of effectuated enrollments.
NYT says one-fifth of those didn't pay in 2014. So if that continued then it's 7, instead of 9 million.
And it makes sense that it would have only been 3 milion or so the first year, and gone up to 7 by now, because the penalty only went into effect for 2015's taxes.
As well, just because 7 million people signed up, or even 9 if you use your number from CMS, it doesn't mean that 7 million new people were covered. It means that 7 million people used that market to get covereage. That's not to say that they didn't have another option prior to the healthcare law. Or even currently have other options but decided to use healthcare.gov
When I worked for REI, I had insurance as a part-timer, but when ACA came that was not possible any longer because the insurance didn't meet the minimum requirements. Those requirements were unimportant to me and many of the people who used that insurance, but in making the changes, REI realized they would not be able to provide it at any sensible cost and cancelled the program. They encouraged us to seek out options on the exchange. When I did that, I found out how much more expsensive that would be, and decided not to carry insurance. I then changed jobs into a position with REI where I was full-time. The other people I know either went onto their spouse's insurance or to the exchange which was dramatically more expensive. But they would be counted for the numbers at healthcare.gov