That's a prediction, not the polls. The polls indicated about a 3-4% preference for Hillary at the national level. She ended up with a 1-2% preference, so the polls were at least as accurate as in the past (nationally at least).

The fact that CNN interpreted the data poorly doesn't mean the data was bad. FiveThirtyEight stated repeatedly that Clinton's lead was not insurmountable and the a typical polling error could easily flip it to Trump.

  She ended up with a 1-2% preference

You are off by an order of magnitude there. As of Wednesday afternoon, the actual popular vote difference was less than 0.17% of votes cast.

No, all we have right now are projections, which put Clinton at ~2% lead in the popular vote. We won't have final vote counts until probably December, because many millions of outstanding votes are still uncounted.

The same thing happens every presidential cycle. Counts come in much slower for populous states with large volumes of absentee, provisional, and mail-in ballots. Clinton is going to win these votes by something like a 2:1 margin.

Looks like you're right according to the Wikipedia total. Last I looked it was expected she'd end up with a 1-2% lead once all the West Coast votes were counted. e.g. The NYT is still showing an estimated 1.2% lead for Clinton in the popular vote. http://www.nytimes.com/elections/forecast/president