When I went to view CNN's analysis the day of the election, it was reporting (on their website) a 90% chance Hillary would win.
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.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.