Take a look at these two stories:
http://www.politifact.com/truth-o-meter/statements/2016/oct/...
http://www.politifact.com/truth-o-meter/statements/2016/sep/...
Now, the first story is simply true. Hillary Clinton did attack her husband's mistresses and accusers, and there's a long history of documentation of that. But Politifact labels it "mostly false" because it was never proven to have come directly from her. As if Sidney Blumenthal just took it upon himself to slander Lewinsky as a delusional nymphomaniac.
In the second link, Clinton claims none of her emails were labelled Top Secret. Note the dodge, here. She didn't say, "I didn't send or receive classified information", she said "those emails didn't contain the correct headers". I wouldn't be surprised in the slightest, given that we know she tried desperately to modify the records of the emails once they were discovered, if those headers were simply stripped either before or after the fact. Either way, she is simply not stupid enough to not know what she was doing. But she claims innocence through stupidity, and politifact labels it "mostly true".
What do both of these examples show? That when Hillary walks the line and is careful not to explicitly say anything demonstrably false, while clearly lying in substance, politifact says she's honest. When Trump says something that's substantively true, while not paying attention to specifics, politifact says he's lying.
This is not intellectually honest fact-checking. Letting one candidate play word games and lie while calling out the other for being less careful but telling the truth is not fact-checking, it's shilling.