The polling models didn't consider how many Libertarians might switch from Johnson to Trump when it came to actual voting. The states which were won by a thin margin were won based on which percentage of the vote Johnson got. PA (which pushed Trump past 270 on the election night) gave only 2% to Johnson. NH (which went to Clinton) gave 4%+ to Johnson. Johnson was polling at 4%-5% the day before the election and he got roughly 3% on the day of the election.
So why did Libertarians, all of a sudden, switch on the day of the election? No one considered what was the central issue to Libertarian voters. They tend to view literal interpretation of the Constitution as canon. Most people who voted for Clinton did not think that her dismissiveness of the law was a high enough priority to consider. Certainly, not higher than everything which they didn't like about Trump.
Regardless of whether her legal troubles were important or not to others, they would be important to Libertarians. They would put a very high priority on keeping out of office someone who viewed legal compliance as optional, at best. So, for a large number of them, keeping Clinton out of office would become a higher priority than making a statement that Libertarian philosophy is a viable political philosophy.
Many of them may not have even liked Trump, but if they thought that he would be more respectful of the rule of law than Clinton would be, pragmatism would have won over principles for a lot of them and caused them to switch their vote when it came time to actually vote.