As near as I can tell, there are two issues.
One is the abscence of a rating and one is the presence of CF on a watch list.
From
http://www.factcheck.org/2015/06/where-does-clinton-foundation-money-go/
(Story linked on CN website)
We spoke by phone with Sandra Minuitti at Charity Navigator, and she told us Charity Navigator decided not to rate the Clinton Foundation because the foundation spun off some entities (chiefly the Health Access Initiative) and then later brought some, like the Clinton Global Initiative, back into the fold. Charity Navigator looks at a charity’s performance over time, she said, and those spin-offs could result in a skewed picture using its analysis model. If the foundation maintains its current structure for several years, she said, Charity Navigator will be able to rate it again.
The decision to withhold a rating had nothing to do with concerns about the Clinton Foundation’s charitable work. Further, Minuitti said citing only the 6 percent of the budget spent on grants as the sum total spent on charity by the foundation — as Willis and Fiorina did — is inaccurate.
I was completely wrong about the reason it was not rated. On the other hand, the accusations of quid-pro-quo are also not the reason it was not rated.
The new stories listed on the CN website are the reasons that the CF is on the CN watch list:
It’s true, as Willis said, that Charity Navigator put the Clinton Foundation on its “watch list,” but not because of concerns about insufficient funds going toward charity. Mainly, it was put on the watch list due to questions raised in the media about foreign donations to the foundation and the potential for quid pro quo when Hillary Clinton was secretary of state. The site also linked to a story about the abrupt resignation earlier this year of the foundation’s CEO. (Go here to see a full list of articles that led to the decision by Charity Navigator to place the foundation on its watch list.)
According to the Charity Navigator site, it “takes no position” on the allegations raised in the media reports, nor does it “seek to confirm or verify the accuracy of allegations made or the merits of issues raised.” Minuitti said the watch list was more like “news to know” for potential donors.
None of the articles cited by Charity Navigator has anything to do with a low percentage of funding going to charitable work.
Same source:
Another philanthropy watchdog, CharityWatch, a project of the American Institute of Philanthropy, gave the Clinton Foundation an “A” rating.
Daniel Borochoff, president and founder of CharityWatch, told us by phone that its analysis of the finances of the Clinton Foundation and its affiliates found that about 89 percent of the foundation budget is spent on programming (or “charity”), higher than the 75 percent considered the industry standard.
So, Charity Navigator official stance is that while the CF one-time divestitures were enough to not give it a rating, the lack of rating "does not indicate a positive or negative assessment by Charity Navigator."