Personally I think 538's prediction was fine. In fact they explicitly called the situation where Trump would win despite the popular vote deficit.
As for the rest of the forecaster that gave Clinton 99% to win, given a US presidential election, the priori of a candidate winning is 50% (historical data, roughly speaking). So you would need some quite extraordinary evidences to get the posterior to 90+% for a candidate.
In this case, the evidences were mostly the polls. To have 99% prediction for a candidate based on a poll, the poll would need have at least 98% accuracy (assuming that when they're wrong, the probability of they being wrong in either directions is the same). Personally, I don't think the polls to be anywhere near that level of accuracy in general. Unfortunately I don't got any number of poll accuracy on hand - I'd love to see it if anyone have a citation.
There are more factors that will affect an election, but with similar reasoning to above, to get a 98-99% prediction, those factors will have to be 90%+ reliable as well. That is some quite tall order.
This is a case where the onus is on the forecaster to show that their number (98% for example) is sound, since they're the one making the extraordinary claim.